Starting phenix.real_space_refine (version: dev) on Mon Feb 20 17:54:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/02_2023/5aey_2850_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/02_2023/5aey_2850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/02_2023/5aey_2850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/02_2023/5aey_2850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/02_2023/5aey_2850_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/02_2023/5aey_2850_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12675 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "B" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "C" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "D" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "E" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.60, per 1000 atoms: 0.60 Number of scatterers: 12675 At special positions: 0 Unit cell: (78.11, 98.44, 181.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 15 15.00 O 2530 8.00 N 2140 7.00 C 7950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.69 Conformation dependent library (CDL) restraints added in 2.0 seconds 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 15 sheets defined 38.1% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.942A pdb=" N GLN A 73 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 116 through 127 removed outlier: 3.816A pdb=" N PHE A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 158 removed outlier: 5.179A pdb=" N GLU A 155 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 4.009A pdb=" N SER A 204 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS A 207 " --> pdb=" O SER A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 227 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 245 through 269 removed outlier: 3.693A pdb=" N GLU A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 removed outlier: 4.082A pdb=" N CYS A 287 " --> pdb=" O GLU A 284 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASP A 288 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 292 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 317 removed outlier: 5.069A pdb=" N LEU A 311 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.957A pdb=" N GLN B 73 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 116 through 127 removed outlier: 3.816A pdb=" N PHE B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 158 removed outlier: 5.183A pdb=" N GLU B 155 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 4.030A pdb=" N SER B 204 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS B 207 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 227 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 245 through 269 removed outlier: 3.661A pdb=" N GLU B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 removed outlier: 4.104A pdb=" N CYS B 287 " --> pdb=" O GLU B 284 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP B 288 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS B 292 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 307 through 317 removed outlier: 5.064A pdb=" N LEU B 311 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.957A pdb=" N GLN C 73 " --> pdb=" O ILE C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 88 Processing helix chain 'C' and resid 116 through 127 removed outlier: 3.818A pdb=" N PHE C 126 " --> pdb=" O LYS C 122 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 158 removed outlier: 5.179A pdb=" N GLU C 155 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 removed outlier: 4.031A pdb=" N SER C 204 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS C 207 " --> pdb=" O SER C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 227 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 245 through 269 removed outlier: 3.650A pdb=" N GLU C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 removed outlier: 4.120A pdb=" N CYS C 287 " --> pdb=" O GLU C 284 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASP C 288 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS C 292 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 307 through 317 removed outlier: 5.060A pdb=" N LEU C 311 " --> pdb=" O GLN C 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.960A pdb=" N GLN D 73 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 88 Processing helix chain 'D' and resid 116 through 127 removed outlier: 3.818A pdb=" N PHE D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 158 removed outlier: 5.176A pdb=" N GLU D 155 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 212 removed outlier: 4.037A pdb=" N SER D 204 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS D 207 " --> pdb=" O SER D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 227 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 245 through 269 removed outlier: 3.660A pdb=" N GLU D 250 " --> pdb=" O SER D 246 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN D 261 " --> pdb=" O ARG D 257 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU D 269 " --> pdb=" O ASN D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 removed outlier: 4.131A pdb=" N CYS D 287 " --> pdb=" O GLU D 284 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASP D 288 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS D 292 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 307 through 317 removed outlier: 5.056A pdb=" N LEU D 311 " --> pdb=" O GLN D 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.949A pdb=" N GLN E 73 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 88 Processing helix chain 'E' and resid 116 through 127 removed outlier: 3.817A pdb=" N PHE E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 158 removed outlier: 5.184A pdb=" N GLU E 155 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 212 removed outlier: 4.039A pdb=" N SER E 204 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LYS E 207 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 227 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 245 through 269 removed outlier: 3.648A pdb=" N GLU E 250 " --> pdb=" O SER E 246 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN E 261 " --> pdb=" O ARG E 257 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU E 269 " --> pdb=" O ASN E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 294 removed outlier: 4.129A pdb=" N CYS E 287 " --> pdb=" O GLU E 284 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASP E 288 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS E 292 " --> pdb=" O ALA E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 307 through 317 removed outlier: 5.059A pdb=" N LEU E 311 " --> pdb=" O GLN E 308 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 22 through 29 removed outlier: 5.514A pdb=" N GLN A 17 " --> pdb=" O LEU A 2 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU A 2 " --> pdb=" O GLN A 17 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP A 97 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE A 5 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL A 99 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASP A 7 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR A 101 " --> pdb=" O ASP A 7 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 49 Processing sheet with id= C, first strand: chain 'A' and resid 275 through 279 removed outlier: 6.306A pdb=" N MET A 182 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE A 188 " --> pdb=" O MET A 182 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 22 through 29 removed outlier: 5.454A pdb=" N GLN B 17 " --> pdb=" O LEU B 2 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU B 2 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASP B 97 " --> pdb=" O VAL B 3 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE B 5 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL B 99 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASP B 7 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N THR B 101 " --> pdb=" O ASP B 7 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 47 through 49 Processing sheet with id= F, first strand: chain 'B' and resid 275 through 279 removed outlier: 6.304A pdb=" N MET B 182 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE B 188 " --> pdb=" O MET B 182 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 22 through 29 removed outlier: 5.483A pdb=" N GLN C 17 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU C 2 " --> pdb=" O GLN C 17 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP C 97 " --> pdb=" O VAL C 3 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE C 5 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL C 99 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASP C 7 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N THR C 101 " --> pdb=" O ASP C 7 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 49 Processing sheet with id= I, first strand: chain 'C' and resid 275 through 279 removed outlier: 6.307A pdb=" N MET C 182 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ILE C 188 " --> pdb=" O MET C 182 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 22 through 29 removed outlier: 5.496A pdb=" N GLN D 17 " --> pdb=" O LEU D 2 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU D 2 " --> pdb=" O GLN D 17 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP D 97 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE D 5 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL D 99 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP D 7 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N THR D 101 " --> pdb=" O ASP D 7 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 47 through 49 Processing sheet with id= L, first strand: chain 'D' and resid 275 through 279 removed outlier: 6.305A pdb=" N MET D 182 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE D 188 " --> pdb=" O MET D 182 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 22 through 29 removed outlier: 5.481A pdb=" N GLN E 17 " --> pdb=" O LEU E 2 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU E 2 " --> pdb=" O GLN E 17 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP E 97 " --> pdb=" O VAL E 3 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE E 5 " --> pdb=" O ASP E 97 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL E 99 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP E 7 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR E 101 " --> pdb=" O ASP E 7 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 47 through 49 Processing sheet with id= O, first strand: chain 'E' and resid 275 through 279 removed outlier: 6.306A pdb=" N MET E 182 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ILE E 188 " --> pdb=" O MET E 182 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 6.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2456 1.32 - 1.45: 3160 1.45 - 1.57: 7164 1.57 - 1.70: 40 1.70 - 1.82: 70 Bond restraints: 12890 Sorted by residual: bond pdb=" C PHE B 4 " pdb=" N ILE B 5 " ideal model delta sigma weight residual 1.329 1.444 -0.115 1.37e-02 5.33e+03 7.07e+01 bond pdb=" N3B ANP B 500 " pdb=" PG ANP B 500 " ideal model delta sigma weight residual 1.795 1.643 0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N3B ANP C 500 " pdb=" PG ANP C 500 " ideal model delta sigma weight residual 1.795 1.645 0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" N3B ANP D 500 " pdb=" PG ANP D 500 " ideal model delta sigma weight residual 1.795 1.647 0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" N3B ANP E 500 " pdb=" PG ANP E 500 " ideal model delta sigma weight residual 1.795 1.648 0.147 2.00e-02 2.50e+03 5.39e+01 ... (remaining 12885 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.67: 379 106.67 - 113.42: 6542 113.42 - 120.18: 5130 120.18 - 126.93: 5291 126.93 - 133.68: 153 Bond angle restraints: 17495 Sorted by residual: angle pdb=" C PHE B 4 " pdb=" N ILE B 5 " pdb=" CA ILE B 5 " ideal model delta sigma weight residual 123.11 112.68 10.43 1.36e+00 5.41e-01 5.88e+01 angle pdb=" N VAL E 66 " pdb=" CA VAL E 66 " pdb=" CB VAL E 66 " ideal model delta sigma weight residual 110.53 117.03 -6.50 1.09e+00 8.42e-01 3.56e+01 angle pdb=" N VAL A 66 " pdb=" CA VAL A 66 " pdb=" CB VAL A 66 " ideal model delta sigma weight residual 110.53 117.02 -6.49 1.09e+00 8.42e-01 3.55e+01 angle pdb=" N VAL C 66 " pdb=" CA VAL C 66 " pdb=" CB VAL C 66 " ideal model delta sigma weight residual 110.53 116.91 -6.38 1.09e+00 8.42e-01 3.42e+01 angle pdb=" N VAL D 66 " pdb=" CA VAL D 66 " pdb=" CB VAL D 66 " ideal model delta sigma weight residual 110.53 116.89 -6.36 1.09e+00 8.42e-01 3.40e+01 ... (remaining 17490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.21: 6956 30.21 - 60.41: 694 60.41 - 90.62: 60 90.62 - 120.83: 0 120.83 - 151.03: 5 Dihedral angle restraints: 7715 sinusoidal: 3090 harmonic: 4625 Sorted by residual: dihedral pdb=" CA LEU B 317 " pdb=" C LEU B 317 " pdb=" N ILE B 318 " pdb=" CA ILE B 318 " ideal model delta harmonic sigma weight residual 180.00 142.63 37.37 0 5.00e+00 4.00e-02 5.59e+01 dihedral pdb=" CA LEU A 317 " pdb=" C LEU A 317 " pdb=" N ILE A 318 " pdb=" CA ILE A 318 " ideal model delta harmonic sigma weight residual 180.00 142.75 37.25 0 5.00e+00 4.00e-02 5.55e+01 dihedral pdb=" CA LEU D 317 " pdb=" C LEU D 317 " pdb=" N ILE D 318 " pdb=" CA ILE D 318 " ideal model delta harmonic sigma weight residual 180.00 142.89 37.11 0 5.00e+00 4.00e-02 5.51e+01 ... (remaining 7712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1180 0.073 - 0.146: 514 0.146 - 0.219: 185 0.219 - 0.292: 84 0.292 - 0.365: 57 Chirality restraints: 2020 Sorted by residual: chirality pdb=" CA ARG A 262 " pdb=" N ARG A 262 " pdb=" C ARG A 262 " pdb=" CB ARG A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA ASN D 268 " pdb=" N ASN D 268 " pdb=" C ASN D 268 " pdb=" CB ASN D 268 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA PHE B 46 " pdb=" N PHE B 46 " pdb=" C PHE B 46 " pdb=" CB PHE B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 2017 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 107 " -0.046 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR E 107 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR E 107 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR E 107 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR E 107 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 107 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 107 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 107 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 107 " -0.046 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR A 107 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 107 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 107 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 107 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 107 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 107 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 107 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 107 " 0.042 2.00e-02 2.50e+03 2.23e-02 9.95e+00 pdb=" CG TYR D 107 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR D 107 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR D 107 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR D 107 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 107 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 107 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 107 " 0.018 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 844 2.74 - 3.28: 13308 3.28 - 3.82: 21668 3.82 - 4.36: 26506 4.36 - 4.90: 41457 Nonbonded interactions: 103783 Sorted by model distance: nonbonded pdb=" N ARG A 297 " pdb=" OD2 ASP C 241 " model vdw 2.197 2.520 nonbonded pdb=" N ARG C 297 " pdb=" OD2 ASP E 241 " model vdw 2.220 2.520 nonbonded pdb=" N ARG B 297 " pdb=" OD2 ASP D 241 " model vdw 2.222 2.520 nonbonded pdb=" O ASP B 164 " pdb=" N GLY B 183 " model vdw 2.303 2.520 nonbonded pdb=" O ASP E 164 " pdb=" N GLY E 183 " model vdw 2.303 2.520 ... (remaining 103778 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 40 5.16 5 C 7950 2.51 5 N 2140 2.21 5 O 2530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.020 Check model and map are aligned: 0.250 Process input model: 35.410 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.130 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.152 12890 Z= 0.737 Angle : 1.714 14.993 17495 Z= 1.035 Chirality : 0.110 0.365 2020 Planarity : 0.006 0.047 2220 Dihedral : 21.882 151.032 4735 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 2.85 % Allowed : 8.67 % Favored : 88.48 % Rotamer Outliers : 18.45 % Cbeta Deviations : 2.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.68 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.18), residues: 1580 helix: -2.13 (0.17), residues: 555 sheet: -1.14 (0.26), residues: 365 loop : -2.70 (0.21), residues: 660 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 370 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 261 outliers final: 78 residues processed: 576 average time/residue: 0.2943 time to fit residues: 229.4729 Evaluate side-chains 303 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 225 time to evaluate : 1.580 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 78 outliers final: 1 residues processed: 78 average time/residue: 0.1653 time to fit residues: 22.8020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 40 optimal weight: 50.0000 chunk 79 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 73 optimal weight: 0.0980 chunk 90 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 83 HIS ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN C 83 HIS ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN D 83 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 253 ASN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN E 83 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 12890 Z= 0.224 Angle : 0.780 10.067 17495 Z= 0.399 Chirality : 0.045 0.218 2020 Planarity : 0.005 0.071 2220 Dihedral : 11.734 159.741 1720 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.18 % Favored : 90.13 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.19), residues: 1580 helix: -0.94 (0.21), residues: 560 sheet: 0.14 (0.29), residues: 325 loop : -2.18 (0.20), residues: 695 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 360 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 366 average time/residue: 0.2836 time to fit residues: 142.8042 Evaluate side-chains 221 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 218 time to evaluate : 1.645 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1331 time to fit residues: 2.8735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 141 optimal weight: 50.0000 chunk 152 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 113 optimal weight: 10.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 261 GLN A 265 ASN B 17 GLN B 115 ASN B 118 ASN B 125 ASN ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN C 308 GLN ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 12890 Z= 0.291 Angle : 0.755 8.957 17495 Z= 0.399 Chirality : 0.046 0.262 2020 Planarity : 0.005 0.050 2220 Dihedral : 11.995 173.439 1720 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.89 % Favored : 88.80 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.20), residues: 1580 helix: -1.05 (0.20), residues: 600 sheet: -0.17 (0.27), residues: 385 loop : -2.12 (0.22), residues: 595 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 278 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 284 average time/residue: 0.2586 time to fit residues: 104.1535 Evaluate side-chains 206 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 1.608 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1368 time to fit residues: 2.6177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 8.9990 chunk 106 optimal weight: 40.0000 chunk 73 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 67 optimal weight: 30.0000 chunk 94 optimal weight: 7.9990 chunk 141 optimal weight: 30.0000 chunk 149 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 40 optimal weight: 50.0000 chunk 124 optimal weight: 30.0000 overall best weight: 10.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 17 GLN ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN A 118 ASN A 125 ASN A 265 ASN B 125 ASN ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN D 78 ASN ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 12890 Z= 0.303 Angle : 0.750 7.916 17495 Z= 0.396 Chirality : 0.045 0.163 2020 Planarity : 0.005 0.058 2220 Dihedral : 12.068 179.119 1720 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.01 % Favored : 88.67 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.20), residues: 1580 helix: -1.24 (0.19), residues: 625 sheet: 0.35 (0.30), residues: 325 loop : -2.41 (0.20), residues: 630 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 259 average time/residue: 0.2493 time to fit residues: 93.0717 Evaluate side-chains 193 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.672 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1714 time to fit residues: 2.5259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 111 optimal weight: 0.0070 chunk 61 optimal weight: 30.0000 chunk 127 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 0.0060 chunk 134 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 overall best weight: 3.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN B 253 ASN B 308 GLN D 308 GLN E 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12890 Z= 0.171 Angle : 0.654 7.031 17495 Z= 0.343 Chirality : 0.043 0.239 2020 Planarity : 0.005 0.078 2220 Dihedral : 11.694 178.945 1720 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.87 % Favored : 89.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.20), residues: 1580 helix: -1.04 (0.20), residues: 590 sheet: 0.33 (0.28), residues: 345 loop : -2.07 (0.22), residues: 645 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2892 time to fit residues: 112.7307 Evaluate side-chains 209 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.666 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.3980 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN A 125 ASN B 253 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12890 Z= 0.189 Angle : 0.656 7.536 17495 Z= 0.343 Chirality : 0.043 0.210 2020 Planarity : 0.005 0.076 2220 Dihedral : 11.639 179.296 1720 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.87 % Favored : 89.81 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.20), residues: 1580 helix: -0.94 (0.21), residues: 580 sheet: 0.19 (0.28), residues: 355 loop : -1.97 (0.22), residues: 645 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 272 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 273 average time/residue: 0.2653 time to fit residues: 102.4503 Evaluate side-chains 206 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 1.606 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1527 time to fit residues: 2.5101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 83 optimal weight: 30.0000 chunk 149 optimal weight: 30.0000 chunk 93 optimal weight: 30.0000 chunk 91 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.6567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 12890 Z= 0.275 Angle : 0.713 6.931 17495 Z= 0.378 Chirality : 0.045 0.208 2020 Planarity : 0.005 0.078 2220 Dihedral : 11.825 178.450 1720 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.95 % Favored : 88.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.20), residues: 1580 helix: -1.10 (0.20), residues: 595 sheet: 0.22 (0.29), residues: 340 loop : -2.03 (0.22), residues: 645 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2562 time to fit residues: 94.0144 Evaluate side-chains 194 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.573 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 30.0000 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 0.0570 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 117 optimal weight: 30.0000 chunk 135 optimal weight: 0.0770 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.6976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 12890 Z= 0.152 Angle : 0.665 8.652 17495 Z= 0.339 Chirality : 0.043 0.225 2020 Planarity : 0.005 0.085 2220 Dihedral : 11.457 176.828 1720 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.92 % Favored : 90.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.20), residues: 1580 helix: -0.92 (0.21), residues: 575 sheet: 0.01 (0.27), residues: 360 loop : -1.79 (0.23), residues: 645 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.2585 time to fit residues: 103.4471 Evaluate side-chains 196 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.662 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 20.0000 chunk 130 optimal weight: 40.0000 chunk 139 optimal weight: 20.0000 chunk 83 optimal weight: 50.0000 chunk 60 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 GLN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN E 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 12890 Z= 0.253 Angle : 0.704 8.315 17495 Z= 0.368 Chirality : 0.044 0.231 2020 Planarity : 0.005 0.072 2220 Dihedral : 11.588 178.478 1720 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.44 % Favored : 89.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.20), residues: 1580 helix: -1.07 (0.20), residues: 585 sheet: 0.18 (0.28), residues: 345 loop : -1.92 (0.23), residues: 650 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.625 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2404 time to fit residues: 85.6188 Evaluate side-chains 191 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 75 optimal weight: 0.0030 chunk 97 optimal weight: 30.0000 overall best weight: 4.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.7189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12890 Z= 0.179 Angle : 0.671 8.529 17495 Z= 0.345 Chirality : 0.043 0.239 2020 Planarity : 0.005 0.065 2220 Dihedral : 11.382 179.413 1720 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.37 % Favored : 90.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.21), residues: 1580 helix: -1.00 (0.21), residues: 580 sheet: 0.01 (0.27), residues: 365 loop : -1.70 (0.24), residues: 635 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.716 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2299 time to fit residues: 84.0913 Evaluate side-chains 190 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.636 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 18 optimal weight: 30.0000 chunk 34 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.091030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.084146 restraints weight = 49424.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.085639 restraints weight = 30301.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086685 restraints weight = 20461.462| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12890 Z= 0.163 Angle : 0.654 8.272 17495 Z= 0.337 Chirality : 0.042 0.228 2020 Planarity : 0.005 0.060 2220 Dihedral : 11.279 177.961 1720 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.49 % Favored : 90.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.21), residues: 1580 helix: -0.80 (0.22), residues: 540 sheet: 0.11 (0.28), residues: 365 loop : -1.46 (0.23), residues: 675 =============================================================================== Job complete usr+sys time: 2549.69 seconds wall clock time: 47 minutes 19.61 seconds (2839.61 seconds total)