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 rotamers | 4.92% |
Goal: <1% |
Ramachandran outliers | 4.35% |
Goal: <0.2% |
Ramachandran favored | 89.86% |
Goal: >98% |
Cβ deviations >0.25Å | 0 |
Goal: 0 |
MolProbity score^ | 3.18 | 17th 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
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 rotamers | 3.28% |
Goal: <1% |
Ramachandran outliers | 1.45% |
Goal: <0.2% |
Ramachandran favored | 94.20% |
Goal: >98% |
Cβ deviations >0.25Å | 0 |
Goal: 0 |
MolProbity score^ | 2.90 | 27th 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
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 rotamers | 3.28% |
Goal: <1% |
Ramachandran outliers | 0.00% |
Goal: <0.2% |
Ramachandran favored | 91.30% |
Goal: >98% |
Cβ deviations >0.25Å | 0 |
Goal: 0 |
MolProbity score^ | 2.96 | 24th 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
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 rotamers | 3.28% |
Goal: <1% |
Ramachandran outliers | 4.35% |
Goal: <0.2% |
Ramachandran favored | 86.96% |
Goal: >98% |
Cβ deviations >0.25Å | 3 |
Goal: 0 |
MolProbity score^ | 3.25 | 15th 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
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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