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Uploaded PDB file as SODEF17.B99990001.pdb
Entry begun:Today at 7:59pm EDT
Last modified:Today at 7:59pm EDT

Your file from local disk was uploaded as SODEF17.B99990001.pdb.
  • 1 chain(s) is/are present [1 unique chain(s)]
  • A total of 71 residues are present.
  • Protein mainchain and sidechains are present.
  • No explicit hydrogen atoms are included.
  • 0 PDBv2.3 atoms were found. Proceeding assuming PDBv3 formatted file.

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Analysis output: all-atom contacts and geometry for SODEF17.B99990001.pdb
Entry begun:Today at 8:00pm EDT
Last modified:Today at 8:00pm EDT

Summary statistics

All-Atom
Contacts
Clashscore, all atoms:41.59 7th percentile* (N=1784, all resolutions)
Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.
Protein
Geometry
Poor rotamers4.92% Goal: <1%
Ramachandran outliers4.35% Goal: <0.2%
Ramachandran favored89.86% Goal: >98%
Cβ deviations >0.25Å0 Goal: 0
MolProbity score^3.1817th percentile* (N=27675, 0Å - 99Å)
Residues with bad bonds:0.00% Goal: 0%
Residues with bad angles:2.82% Goal: <0.1%
* 100th percentile is the best among structures of comparable resolution; 0th percentile is the worst.
^ MolProbity score is defined as the following: 0.42574*log(1+clashscore) + 0.32996*log(1+max(0,pctRotOut-1)) + 0.24979*log(1+max(0,100-pctRamaFavored-2)) + 0.5

Multi-criterion visualizations

Kinemage (683 Kb)
View in KiNG | Download (683 Kb)
Chart (66 Kb)
View (66 Kb)

Single-criterion visualizations

REMARK 40

You can download your PDB file with REMARK 40 inserted, or the same without hydrogens.

REMARK  40                                                                      
REMARK  40 MOLPROBITY STRUCTURE VALIDATION                                      
REMARK  40  PROGRAMS    : MOLPROBITY  (KING, REDUCE, AND PROBE)                 
REMARK  40  AUTHORS     : I.W.DAVIS,V.B.CHEN,                                   
REMARK  40              : R.M.IMMORMINO,J.J.HEADD,W.B.ARENDALL,J.M.WORD         
REMARK  40  URL         : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/          
REMARK  40  AUTHORS     : I.W.DAVIS,A.LEAVER-FAY,V.B.CHEN,J.N.BLOCK,            
REMARK  40              : G.J.KAPRAL,X.WANG,L.W.MURRAY,W.B.ARENDALL,            
REMARK  40              : J.SNOEYINK,J.S.RICHARDSON,D.C.RICHARDSON              
REMARK  40  REFERENCE   : MOLPROBITY: ALL-ATOM CONTACTS AND STRUCTURE           
REMARK  40              : VALIDATION FOR PROTEINS AND NUCLEIC ACIDS             
REMARK  40              : NUCLEIC ACIDS RESEARCH. 2007;35:W375-83.              
REMARK  40  MOLPROBITY OUTPUT SCORES:                                           
REMARK  40  ALL-ATOM CLASHSCORE     :  41.59                                    
REMARK  40  BAD ROTAMERS            :   4.9%    3/61     (TARGET  0-1%)         
REMARK  40  RAMACHANDRAN OUTLIERS   :   4.3%    3/69     (TARGET  0.2%)         
REMARK  40  RAMACHANDRAN FAVORED    :  89.9%   62/69     (TARGET 98.0%)         

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Uploaded PDB file as SODEF17.B99990002.pdb
Entry begun:Today at 8:01pm EDT
Last modified:Today at 8:01pm EDT

Your file from local disk was uploaded as SODEF17.B99990002.pdb.
  • 1 chain(s) is/are present [1 unique chain(s)]
  • A total of 71 residues are present.
  • Protein mainchain and sidechains are present.
  • No explicit hydrogen atoms are included.
  • 0 PDBv2.3 atoms were found. Proceeding assuming PDBv3 formatted file.

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Analysis output: all-atom contacts and geometry for SODEF17.B99990002.pdb
Entry begun:Today at 8:01pm EDT
Last modified:Today at 8:01pm EDT

Summary statistics

All-Atom
Contacts
Clashscore, all atoms:43.4 6th percentile* (N=1784, all resolutions)
Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.
Protein
Geometry
Poor rotamers3.28% Goal: <1%
Ramachandran outliers1.45% Goal: <0.2%
Ramachandran favored94.20% Goal: >98%
Cβ deviations >0.25Å0 Goal: 0
MolProbity score^2.9027th percentile* (N=27675, 0Å - 99Å)
Residues with bad bonds:0.00% Goal: 0%
Residues with bad angles:0.00% Goal: <0.1%
* 100th percentile is the best among structures of comparable resolution; 0th percentile is the worst.
^ MolProbity score is defined as the following: 0.42574*log(1+clashscore) + 0.32996*log(1+max(0,pctRotOut-1)) + 0.24979*log(1+max(0,100-pctRamaFavored-2)) + 0.5

Multi-criterion visualizations

Kinemage (605 Kb)
View in KiNG | Download (605 Kb)
Chart (66 Kb)
View (66 Kb)

Single-criterion visualizations

REMARK 40

You can download your PDB file with REMARK 40 inserted, or the same without hydrogens.

REMARK  40                                                                      
REMARK  40 MOLPROBITY STRUCTURE VALIDATION                                      
REMARK  40  PROGRAMS    : MOLPROBITY  (KING, REDUCE, AND PROBE)                 
REMARK  40  AUTHORS     : I.W.DAVIS,V.B.CHEN,                                   
REMARK  40              : R.M.IMMORMINO,J.J.HEADD,W.B.ARENDALL,J.M.WORD         
REMARK  40  URL         : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/          
REMARK  40  AUTHORS     : I.W.DAVIS,A.LEAVER-FAY,V.B.CHEN,J.N.BLOCK,            
REMARK  40              : G.J.KAPRAL,X.WANG,L.W.MURRAY,W.B.ARENDALL,            
REMARK  40              : J.SNOEYINK,J.S.RICHARDSON,D.C.RICHARDSON              
REMARK  40  REFERENCE   : MOLPROBITY: ALL-ATOM CONTACTS AND STRUCTURE           
REMARK  40              : VALIDATION FOR PROTEINS AND NUCLEIC ACIDS             
REMARK  40              : NUCLEIC ACIDS RESEARCH. 2007;35:W375-83.              
REMARK  40  MOLPROBITY OUTPUT SCORES:                                           
REMARK  40  ALL-ATOM CLASHSCORE     :  43.40                                    
REMARK  40  BAD ROTAMERS            :   3.3%    2/61     (TARGET  0-1%)         
REMARK  40  RAMACHANDRAN OUTLIERS   :   1.4%    1/69     (TARGET  0.2%)         
REMARK  40  RAMACHANDRAN FAVORED    :  94.2%   65/69     (TARGET 98.0%)         

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Uploaded PDB file as SODEF17.B99990003.pdb
Entry begun:Today at 8:02pm EDT
Last modified:Today at 8:02pm EDT

Your file from local disk was uploaded as SODEF17.B99990003.pdb.
  • 1 chain(s) is/are present [1 unique chain(s)]
  • A total of 71 residues are present.
  • Protein mainchain and sidechains are present.
  • No explicit hydrogen atoms are included.
  • 0 PDBv2.3 atoms were found. Proceeding assuming PDBv3 formatted file.

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Analysis output: all-atom contacts and geometry for SODEF17.B99990003.pdb
Entry begun:Today at 8:03pm EDT
Last modified:Today at 8:03pm EDT

Summary statistics

All-Atom
Contacts
Clashscore, all atoms:37.97 9th percentile* (N=1784, all resolutions)
Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.
Protein
Geometry
Poor rotamers3.28% Goal: <1%
Ramachandran outliers0.00% Goal: <0.2%
Ramachandran favored91.30% Goal: >98%
Cβ deviations >0.25Å0 Goal: 0
MolProbity score^2.9624th percentile* (N=27675, 0Å - 99Å)
Residues with bad bonds:0.00% Goal: 0%
Residues with bad angles:1.41% Goal: <0.1%
* 100th percentile is the best among structures of comparable resolution; 0th percentile is the worst.
^ MolProbity score is defined as the following: 0.42574*log(1+clashscore) + 0.32996*log(1+max(0,pctRotOut-1)) + 0.24979*log(1+max(0,100-pctRamaFavored-2)) + 0.5

Multi-criterion visualizations

Kinemage (707 Kb)
View in KiNG | Download (707 Kb)
Chart (66 Kb)
View (66 Kb)

Single-criterion visualizations

REMARK 40

You can download your PDB file with REMARK 40 inserted, or the same without hydrogens.

REMARK  40                                                                      
REMARK  40 MOLPROBITY STRUCTURE VALIDATION                                      
REMARK  40  PROGRAMS    : MOLPROBITY  (KING, REDUCE, AND PROBE)                 
REMARK  40  AUTHORS     : I.W.DAVIS,V.B.CHEN,                                   
REMARK  40              : R.M.IMMORMINO,J.J.HEADD,W.B.ARENDALL,J.M.WORD         
REMARK  40  URL         : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/          
REMARK  40  AUTHORS     : I.W.DAVIS,A.LEAVER-FAY,V.B.CHEN,J.N.BLOCK,            
REMARK  40              : G.J.KAPRAL,X.WANG,L.W.MURRAY,W.B.ARENDALL,            
REMARK  40              : J.SNOEYINK,J.S.RICHARDSON,D.C.RICHARDSON              
REMARK  40  REFERENCE   : MOLPROBITY: ALL-ATOM CONTACTS AND STRUCTURE           
REMARK  40              : VALIDATION FOR PROTEINS AND NUCLEIC ACIDS             
REMARK  40              : NUCLEIC ACIDS RESEARCH. 2007;35:W375-83.              
REMARK  40  MOLPROBITY OUTPUT SCORES:                                           
REMARK  40  ALL-ATOM CLASHSCORE     :  37.97                                    
REMARK  40  BAD ROTAMERS            :   3.3%    2/61     (TARGET  0-1%)         
REMARK  40  RAMACHANDRAN OUTLIERS   :   0.0%    0/69     (TARGET  0.2%)         
REMARK  40  RAMACHANDRAN FAVORED    :  91.3%   63/69     (TARGET 98.0%)         

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Uploaded PDB file as cluster.opt.pdb
Entry begun:Today at 8:04pm EDT
Last modified:Today at 8:04pm EDT

Your file from local disk was uploaded as cluster.opt.pdb.
  • 1 chain(s) is/are present [1 unique chain(s)]
  • A total of 71 residues are present.
  • Protein mainchain and sidechains are present.
  • No explicit hydrogen atoms are included.
  • 0 PDBv2.3 atoms were found. Proceeding assuming PDBv3 formatted file.

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Analysis output: all-atom contacts and geometry for cluster.opt.pdb
Entry begun:Today at 8:04pm EDT
Last modified:Today at 8:04pm EDT

Summary statistics

All-Atom
Contacts
Clashscore, all atoms:57.87 2nd percentile* (N=1784, all resolutions)
Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.
Protein
Geometry
Poor rotamers3.28% Goal: <1%
Ramachandran outliers4.35% Goal: <0.2%
Ramachandran favored86.96% Goal: >98%
Cβ deviations >0.25Å3 Goal: 0
MolProbity score^3.2515th percentile* (N=27675, 0Å - 99Å)
Residues with bad bonds:0.00% Goal: 0%
Residues with bad angles:8.45% Goal: <0.1%
* 100th percentile is the best among structures of comparable resolution; 0th percentile is the worst.
^ MolProbity score is defined as the following: 0.42574*log(1+clashscore) + 0.32996*log(1+max(0,pctRotOut-1)) + 0.24979*log(1+max(0,100-pctRamaFavored-2)) + 0.5

Multi-criterion visualizations

Kinemage (750 Kb)
View in KiNG | Download (750 Kb)
Chart (67 Kb)
View (67 Kb)

Single-criterion visualizations

REMARK 40

You can download your PDB file with REMARK 40 inserted, or the same without hydrogens.

REMARK  40                                                                      
REMARK  40 MOLPROBITY STRUCTURE VALIDATION                                      
REMARK  40  PROGRAMS    : MOLPROBITY  (KING, REDUCE, AND PROBE)                 
REMARK  40  AUTHORS     : I.W.DAVIS,V.B.CHEN,                                   
REMARK  40              : R.M.IMMORMINO,J.J.HEADD,W.B.ARENDALL,J.M.WORD         
REMARK  40  URL         : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/          
REMARK  40  AUTHORS     : I.W.DAVIS,A.LEAVER-FAY,V.B.CHEN,J.N.BLOCK,            
REMARK  40              : G.J.KAPRAL,X.WANG,L.W.MURRAY,W.B.ARENDALL,            
REMARK  40              : J.SNOEYINK,J.S.RICHARDSON,D.C.RICHARDSON              
REMARK  40  REFERENCE   : MOLPROBITY: ALL-ATOM CONTACTS AND STRUCTURE           
REMARK  40              : VALIDATION FOR PROTEINS AND NUCLEIC ACIDS             
REMARK  40              : NUCLEIC ACIDS RESEARCH. 2007;35:W375-83.              
REMARK  40  MOLPROBITY OUTPUT SCORES:                                           
REMARK  40  ALL-ATOM CLASHSCORE     :  57.87                                    
REMARK  40  BAD ROTAMERS            :   3.3%    2/61     (TARGET  0-1%)         
REMARK  40  RAMACHANDRAN OUTLIERS   :   4.3%    3/69     (TARGET  0.2%)         
REMARK  40  RAMACHANDRAN FAVORED    :  87.0%   60/69     (TARGET 98.0%)         

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