Analysis output: all-atom contacts and geometry for rcsb059929.pdb

Summary statistics

All-Atom
Contacts Clashscore, all atoms: 7.01 93^rd percentile^* (N=715, 2.00Å ± 0.25Å)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 1.39% Goal: <1%

Ramachandran outliers 0.00% Goal: <0.2%

Ramachandran favored 98.41% Goal: >98%

Cβ deviations >0.25Å 0 Goal: 0

MolProbity score^{^} 1.49 97^th percentile^* (N=12522, 2.00Å ± 0.25Å)

Residues with bad bonds: 0.00% Goal: 0%

Residues with bad angles: 0.00% Goal: <0.1%

* 100^th percentile is the best among structures of comparable resolution; 0^th 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

View (640 Kb)

Single-criterion visualizations

Clash list (4 Kb): View
Ramachandran plot kinemage (367 Kb): View in KiNG | Download
Ramachandran plot PDF (206 Kb): View
Cβ deviation scatter plot (40 Kb): View in KiNG | Download

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     :   7.01                                    
REMARK  40  BAD ROTAMERS            :   1.4%    7/503    (TARGET  0-1%)         
REMARK  40  RAMACHANDRAN OUTLIERS   :   0.0%    0/567    (TARGET  0.2%)         
REMARK  40  RAMACHANDRAN FAVORED    :  98.4%  558/567    (TARGET 98.0%)