Starting phenix.real_space_refine (version: dev) on Sat May 14 02:20:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiq_0227/05_2022/6hiq_0227_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiq_0227/05_2022/6hiq_0227.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiq_0227/05_2022/6hiq_0227_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiq_0227/05_2022/6hiq_0227_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiq_0227/05_2022/6hiq_0227_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiq_0227/05_2022/6hiq_0227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiq_0227/05_2022/6hiq_0227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiq_0227/05_2022/6hiq_0227_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiq_0227/05_2022/6hiq_0227_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.007 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 16110 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3139 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3139 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3139 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3139 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3139 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 83 Unusual residues: {'NAG': 5, 'SRO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 83 Unusual residues: {'NAG': 5, 'SRO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 83 Unusual residues: {'NAG': 5, 'SRO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 83 Unusual residues: {'NAG': 5, 'SRO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 83 Unusual residues: {'NAG': 5, 'SRO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 9.19, per 1000 atoms: 0.57 Number of scatterers: 16110 At special positions: 0 Unit cell: (97.097, 94.963, 165.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 2890 8.00 N 2595 7.00 C 10580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 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 Links applied BETA1-4 " NAG A 502 " - " NAG A 503 " " NAG A 504 " - " NAG A 505 " " NAG B 502 " - " NAG B 503 " " NAG B 504 " - " NAG B 505 " " NAG C 502 " - " NAG C 503 " " NAG C 504 " - " NAG C 505 " " NAG D 502 " - " NAG D 503 " " NAG D 504 " - " NAG D 505 " " NAG E 502 " - " NAG E 503 " " NAG E 504 " - " NAG E 505 " NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG A 503 " - " ASN A 164 " " NAG A 504 " - " ASN A 148 " " NAG B 501 " - " ASN B 82 " " NAG B 503 " - " ASN B 164 " " NAG B 504 " - " ASN B 148 " " NAG C 501 " - " ASN C 82 " " NAG C 503 " - " ASN C 164 " " NAG C 504 " - " ASN C 148 " " NAG D 501 " - " ASN D 82 " " NAG D 503 " - " ASN D 164 " " NAG D 504 " - " ASN D 148 " " NAG E 501 " - " ASN E 82 " " NAG E 503 " - " ASN E 164 " " NAG E 504 " - " ASN E 148 " Time building additional restraints: 6.95 Conformation dependent library (CDL) restraints added in 2.5 seconds 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 25 sheets defined 40.3% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 removed outlier: 3.628A pdb=" N LEU A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.712A pdb=" N ARG A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 175' Processing helix chain 'A' and resid 224 through 227 No H-bonds generated for 'chain 'A' and resid 224 through 227' Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.504A pdb=" N MET A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 251 through 268 removed outlier: 3.588A pdb=" N ILE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 307 removed outlier: 3.647A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 331 removed outlier: 3.863A pdb=" N HIS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 459 removed outlier: 3.505A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 19 removed outlier: 3.628A pdb=" N LEU E 15 " --> pdb=" O ALA E 11 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.712A pdb=" N ARG E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 171 through 175' Processing helix chain 'E' and resid 224 through 227 No H-bonds generated for 'chain 'E' and resid 224 through 227' Processing helix chain 'E' and resid 229 through 243 removed outlier: 3.503A pdb=" N MET E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE E 242 " --> pdb=" O ASP E 238 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYS E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 248 No H-bonds generated for 'chain 'E' and resid 246 through 248' Processing helix chain 'E' and resid 251 through 268 removed outlier: 3.588A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 307 removed outlier: 3.647A pdb=" N TYR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU E 294 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 331 removed outlier: 3.862A pdb=" N HIS E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE E 329 " --> pdb=" O VAL E 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 459 removed outlier: 3.505A pdb=" N SER E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG E 410 " --> pdb=" O LEU E 406 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 413 " --> pdb=" O ILE E 409 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL E 429 " --> pdb=" O ASP E 425 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU E 436 " --> pdb=" O VAL E 432 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 437 " --> pdb=" O LEU E 433 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR E 448 " --> pdb=" O ALA E 444 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE E 450 " --> pdb=" O LEU E 446 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR E 451 " --> pdb=" O ALA E 447 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 452 " --> pdb=" O TYR E 448 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL E 453 " --> pdb=" O SER E 449 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 19 removed outlier: 3.627A pdb=" N LEU B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.712A pdb=" N ARG B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 175' Processing helix chain 'B' and resid 224 through 227 No H-bonds generated for 'chain 'B' and resid 224 through 227' Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.504A pdb=" N MET B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYS B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 251 through 268 removed outlier: 3.588A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 307 removed outlier: 3.647A pdb=" N TYR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 294 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 331 removed outlier: 3.863A pdb=" N HIS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 459 removed outlier: 3.504A pdb=" N SER B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 436 " --> pdb=" O VAL B 432 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 453 " --> pdb=" O SER B 449 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 19 removed outlier: 3.628A pdb=" N LEU C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.712A pdb=" N ARG C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 171 through 175' Processing helix chain 'C' and resid 224 through 227 No H-bonds generated for 'chain 'C' and resid 224 through 227' Processing helix chain 'C' and resid 229 through 243 removed outlier: 3.504A pdb=" N MET C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYS C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'C' and resid 251 through 268 removed outlier: 3.588A pdb=" N ILE C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 307 removed outlier: 3.647A pdb=" N TYR C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 294 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 331 removed outlier: 3.862A pdb=" N HIS C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 459 removed outlier: 3.505A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 436 " --> pdb=" O VAL C 432 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 437 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL C 453 " --> pdb=" O SER C 449 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 19 removed outlier: 3.628A pdb=" N LEU D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.712A pdb=" N ARG D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 171 through 175' Processing helix chain 'D' and resid 224 through 227 No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 229 through 243 removed outlier: 3.504A pdb=" N MET D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 248 No H-bonds generated for 'chain 'D' and resid 246 through 248' Processing helix chain 'D' and resid 251 through 268 removed outlier: 3.588A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 307 removed outlier: 3.647A pdb=" N TYR D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 294 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 331 removed outlier: 3.863A pdb=" N HIS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 329 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 459 removed outlier: 3.506A pdb=" N SER D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 429 " --> pdb=" O ASP D 425 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 436 " --> pdb=" O VAL D 432 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 437 " --> pdb=" O LEU D 433 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR D 451 " --> pdb=" O ALA D 447 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL D 453 " --> pdb=" O SER D 449 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.184A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 65 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 50 through 52 removed outlier: 3.672A pdb=" N ASN A 50 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 85 through 89 Processing sheet with id= D, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 146 through 149 removed outlier: 3.620A pdb=" N ILE A 216 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 163 through 167 removed outlier: 6.184A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG E 65 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 50 through 52 removed outlier: 3.672A pdb=" N ASN E 50 " --> pdb=" O THR E 59 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= I, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.620A pdb=" N ILE E 216 " --> pdb=" O GLN E 147 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.184A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 65 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 50 through 52 removed outlier: 3.672A pdb=" N ASN B 50 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 85 through 89 Processing sheet with id= N, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 146 through 149 removed outlier: 3.619A pdb=" N ILE B 216 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.183A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 65 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 50 through 52 removed outlier: 3.672A pdb=" N ASN C 50 " --> pdb=" O THR C 59 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 85 through 89 Processing sheet with id= S, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.128A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 146 through 149 removed outlier: 3.621A pdb=" N ILE C 216 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.184A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 65 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 50 through 52 removed outlier: 3.672A pdb=" N ASN D 50 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 85 through 89 Processing sheet with id= X, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 146 through 149 removed outlier: 3.620A pdb=" N ILE D 216 " --> pdb=" O GLN D 147 " (cutoff:3.500A) 605 hydrogen bonds defined for protein. 1770 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: 4.98 Time building geometry restraints manager: 7.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4883 1.34 - 1.46: 3525 1.46 - 1.58: 8067 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 16545 Sorted by residual: bond pdb=" CG LEU C 129 " pdb=" CD1 LEU C 129 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.21e+00 bond pdb=" CG LEU A 129 " pdb=" CD1 LEU A 129 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.20e+00 bond pdb=" CG LEU E 129 " pdb=" CD1 LEU E 129 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.19e+00 bond pdb=" CG LEU D 129 " pdb=" CD1 LEU D 129 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.15e+00 bond pdb=" CG LEU B 129 " pdb=" CD1 LEU B 129 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.11e+00 ... (remaining 16540 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.74: 590 106.74 - 113.78: 9442 113.78 - 120.82: 7225 120.82 - 127.86: 5133 127.86 - 134.91: 220 Bond angle restraints: 22610 Sorted by residual: angle pdb=" OH SRO E 506 " pdb=" CZ3 SRO E 506 " pdb=" CH2 SRO E 506 " ideal model delta sigma weight residual 109.40 121.93 -12.53 3.00e+00 1.11e-01 1.74e+01 angle pdb=" OH SRO D 506 " pdb=" CZ3 SRO D 506 " pdb=" CH2 SRO D 506 " ideal model delta sigma weight residual 109.40 121.92 -12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" OH SRO C 506 " pdb=" CZ3 SRO C 506 " pdb=" CH2 SRO C 506 " ideal model delta sigma weight residual 109.40 121.92 -12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" OH SRO A 506 " pdb=" CZ3 SRO A 506 " pdb=" CH2 SRO A 506 " ideal model delta sigma weight residual 109.40 121.92 -12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" OH SRO B 506 " pdb=" CZ3 SRO B 506 " pdb=" CH2 SRO B 506 " ideal model delta sigma weight residual 109.40 121.90 -12.50 3.00e+00 1.11e-01 1.73e+01 ... (remaining 22605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.95: 8884 12.95 - 25.90: 581 25.90 - 38.85: 190 38.85 - 51.79: 10 51.79 - 64.74: 10 Dihedral angle restraints: 9675 sinusoidal: 3935 harmonic: 5740 Sorted by residual: dihedral pdb=" CA GLN D 66 " pdb=" C GLN D 66 " pdb=" N TYR D 67 " pdb=" CA TYR D 67 " ideal model delta harmonic sigma weight residual 180.00 153.18 26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA GLN A 66 " pdb=" C GLN A 66 " pdb=" N TYR A 67 " pdb=" CA TYR A 67 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA GLN B 66 " pdb=" C GLN B 66 " pdb=" N TYR B 67 " pdb=" CA TYR B 67 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 9672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1851 0.055 - 0.111: 631 0.111 - 0.166: 168 0.166 - 0.222: 25 0.222 - 0.277: 5 Chirality restraints: 2680 Sorted by residual: chirality pdb=" CB ILE D 139 " pdb=" CA ILE D 139 " pdb=" CG1 ILE D 139 " pdb=" CG2 ILE D 139 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE C 139 " pdb=" CA ILE C 139 " pdb=" CG1 ILE C 139 " pdb=" CG2 ILE C 139 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CB ILE B 139 " pdb=" CA ILE B 139 " pdb=" CG1 ILE B 139 " pdb=" CG2 ILE B 139 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2677 not shown) Planarity restraints: 2770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 168 " -0.015 2.00e-02 2.50e+03 1.68e-02 7.07e+00 pdb=" CG TRP B 168 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 168 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 168 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 168 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 168 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 168 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 168 " -0.016 2.00e-02 2.50e+03 1.68e-02 7.05e+00 pdb=" CG TRP C 168 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C 168 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 168 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 168 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 168 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 168 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 168 " -0.015 2.00e-02 2.50e+03 1.68e-02 7.03e+00 pdb=" CG TRP A 168 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 168 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 168 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 168 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 168 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 168 " -0.001 2.00e-02 2.50e+03 ... (remaining 2767 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 5007 2.84 - 3.35: 14073 3.35 - 3.87: 25986 3.87 - 4.38: 29595 4.38 - 4.90: 50077 Nonbonded interactions: 124738 Sorted by model distance: nonbonded pdb=" OE2 GLU D 53 " pdb=" NH2 ARG D 218 " model vdw 2.319 2.520 nonbonded pdb=" OE2 GLU E 53 " pdb=" NH2 ARG E 218 " model vdw 2.319 2.520 nonbonded pdb=" OE2 GLU A 53 " pdb=" NH2 ARG A 218 " model vdw 2.320 2.520 nonbonded pdb=" OE2 GLU C 53 " pdb=" NH2 ARG C 218 " model vdw 2.320 2.520 nonbonded pdb=" OE2 GLU B 53 " pdb=" NH2 ARG B 218 " model vdw 2.320 2.520 ... (remaining 124733 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 10580 2.51 5 N 2595 2.21 5 O 2890 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 individual isotropic 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: 1.170 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: 4.440 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.150 Process input model: 43.720 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.006 0.064 16545 Z= 0.409 Angle : 1.077 12.528 22610 Z= 0.528 Chirality : 0.060 0.277 2680 Planarity : 0.006 0.055 2755 Dihedral : 9.902 64.742 5920 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer Outliers : 0.29 % 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: -4.97 (0.14), residues: 1905 helix: -4.19 (0.09), residues: 685 sheet: -2.40 (0.22), residues: 405 loop : -2.76 (0.18), residues: 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 274 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 279 average time/residue: 0.3869 time to fit residues: 145.7060 Evaluate side-chains 134 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.146 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 57 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 118 HIS A 130 GLN A 147 GLN A 158 HIS E 56 GLN E 118 HIS E 130 GLN E 147 GLN E 460 HIS B 56 GLN B 118 HIS B 130 GLN B 147 GLN B 460 HIS C 56 GLN C 118 HIS C 130 GLN C 147 GLN C 460 HIS D 56 GLN D 118 HIS D 130 GLN D 147 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 16545 Z= 0.240 Angle : 0.692 8.596 22610 Z= 0.347 Chirality : 0.046 0.175 2680 Planarity : 0.005 0.038 2755 Dihedral : 5.784 22.719 2265 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 2.49 % 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: -2.96 (0.17), residues: 1905 helix: -1.43 (0.16), residues: 705 sheet: -2.40 (0.21), residues: 465 loop : -1.94 (0.22), residues: 735 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 161 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 19 residues processed: 196 average time/residue: 0.2811 time to fit residues: 82.5368 Evaluate side-chains 133 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 2.037 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1602 time to fit residues: 8.3183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.0070 chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 153 optimal weight: 0.0170 chunk 171 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 HIS E 460 HIS B 460 HIS C 460 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.115 16545 Z= 0.238 Angle : 0.640 10.330 22610 Z= 0.315 Chirality : 0.044 0.159 2680 Planarity : 0.004 0.031 2755 Dihedral : 5.249 20.608 2265 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 2.66 % 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: -1.65 (0.19), residues: 1905 helix: 0.24 (0.19), residues: 710 sheet: -2.04 (0.22), residues: 450 loop : -1.65 (0.24), residues: 745 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 142 time to evaluate : 1.696 Fit side-chains outliers start: 46 outliers final: 12 residues processed: 181 average time/residue: 0.2808 time to fit residues: 78.0497 Evaluate side-chains 120 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.990 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2118 time to fit residues: 6.7416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 0.2980 chunk 116 optimal weight: 0.0050 chunk 173 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 HIS B 56 GLN C 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.129 16545 Z= 0.247 Angle : 0.596 8.099 22610 Z= 0.298 Chirality : 0.044 0.171 2680 Planarity : 0.004 0.028 2755 Dihedral : 5.069 19.813 2265 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 2.49 % 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: -1.04 (0.20), residues: 1905 helix: 0.96 (0.20), residues: 710 sheet: -1.81 (0.23), residues: 450 loop : -1.48 (0.24), residues: 745 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 122 time to evaluate : 1.985 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 15 residues processed: 156 average time/residue: 0.2548 time to fit residues: 62.0614 Evaluate side-chains 117 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 1.988 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1795 time to fit residues: 7.1233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 2 optimal weight: 0.0060 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN E 56 GLN D 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.130 16545 Z= 0.269 Angle : 0.608 10.575 22610 Z= 0.301 Chirality : 0.044 0.158 2680 Planarity : 0.004 0.027 2755 Dihedral : 4.970 19.055 2265 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 2.25 % 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: -0.68 (0.20), residues: 1905 helix: 1.37 (0.20), residues: 710 sheet: -1.65 (0.24), residues: 450 loop : -1.40 (0.24), residues: 745 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 113 time to evaluate : 2.005 Fit side-chains outliers start: 39 outliers final: 19 residues processed: 147 average time/residue: 0.2558 time to fit residues: 58.7161 Evaluate side-chains 118 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.964 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1667 time to fit residues: 8.1708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 411 HIS ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.121 16545 Z= 0.357 Angle : 0.661 9.900 22610 Z= 0.331 Chirality : 0.047 0.164 2680 Planarity : 0.004 0.029 2755 Dihedral : 5.147 19.453 2265 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 1.79 % 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: -0.51 (0.20), residues: 1905 helix: 1.56 (0.20), residues: 705 sheet: -1.64 (0.23), residues: 455 loop : -1.26 (0.24), residues: 745 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.870 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 16 residues processed: 144 average time/residue: 0.2841 time to fit residues: 63.3333 Evaluate side-chains 117 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 2.100 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1470 time to fit residues: 7.1183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 154 optimal weight: 0.0000 chunk 102 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 111 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 411 HIS ** D 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.133 16545 Z= 0.277 Angle : 0.614 9.105 22610 Z= 0.309 Chirality : 0.044 0.165 2680 Planarity : 0.004 0.039 2755 Dihedral : 4.996 19.115 2265 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.64 % 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: -0.44 (0.20), residues: 1905 helix: 1.56 (0.19), residues: 740 sheet: -1.80 (0.23), residues: 450 loop : -1.16 (0.25), residues: 715 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 2.094 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 122 average time/residue: 0.2867 time to fit residues: 54.0577 Evaluate side-chains 103 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 2.100 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1417 time to fit residues: 4.0226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 119 HIS E 411 HIS C 130 GLN D 119 HIS ** D 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.145 16545 Z= 0.351 Angle : 0.666 10.527 22610 Z= 0.339 Chirality : 0.046 0.164 2680 Planarity : 0.004 0.060 2755 Dihedral : 5.062 19.087 2265 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.75 % 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: -0.37 (0.20), residues: 1905 helix: 1.62 (0.19), residues: 740 sheet: -1.80 (0.23), residues: 450 loop : -1.08 (0.25), residues: 715 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 115 average time/residue: 0.2921 time to fit residues: 51.2089 Evaluate side-chains 105 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 1.997 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1378 time to fit residues: 5.0203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.0980 chunk 170 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 102 optimal weight: 0.0570 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 154 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 411 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.177 16545 Z= 0.307 Angle : 0.648 13.498 22610 Z= 0.342 Chirality : 0.044 0.170 2680 Planarity : 0.004 0.066 2755 Dihedral : 4.794 18.968 2265 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.23 % 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: -0.21 (0.20), residues: 1905 helix: 1.84 (0.20), residues: 740 sheet: -1.77 (0.23), residues: 450 loop : -1.06 (0.25), residues: 715 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 125 average time/residue: 0.3093 time to fit residues: 58.6609 Evaluate side-chains 103 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 2.045 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1387 time to fit residues: 3.0210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 160 optimal weight: 0.2980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.336 16545 Z= 0.411 Angle : 0.725 18.382 22610 Z= 0.389 Chirality : 0.045 0.156 2680 Planarity : 0.005 0.101 2755 Dihedral : 4.850 18.590 2265 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.23 % 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: -0.12 (0.20), residues: 1905 helix: 1.90 (0.20), residues: 740 sheet: -1.71 (0.24), residues: 450 loop : -1.01 (0.25), residues: 715 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 2.007 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 108 average time/residue: 0.2982 time to fit residues: 48.8002 Evaluate side-chains 100 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 1.980 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1382 time to fit residues: 3.3939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 27 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.122989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.086412 restraints weight = 26464.439| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.11 r_work: 0.3041 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.3018 rms_B_bonded: 1.90 restraints_weight: 0.1250 r_work: 0.3005 rms_B_bonded: 1.98 restraints_weight: 0.0625 r_work: 0.2991 rms_B_bonded: 2.09 restraints_weight: 0.0312 r_work: 0.2976 rms_B_bonded: 2.25 restraints_weight: 0.0156 r_work: 0.2960 rms_B_bonded: 2.44 restraints_weight: 0.0078 r_work: 0.2942 rms_B_bonded: 2.68 restraints_weight: 0.0039 r_work: 0.2922 rms_B_bonded: 2.97 restraints_weight: 0.0020 r_work: 0.2900 rms_B_bonded: 3.32 restraints_weight: 0.0010 r_work: 0.2875 rms_B_bonded: 3.74 restraints_weight: 0.0005 r_work: 0.2848 rms_B_bonded: 4.23 restraints_weight: 0.0002 r_work: 0.2817 rms_B_bonded: 4.82 restraints_weight: 0.0001 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.181 16545 Z= 0.247 Angle : 0.647 17.540 22610 Z= 0.336 Chirality : 0.044 0.167 2680 Planarity : 0.005 0.103 2755 Dihedral : 4.682 18.468 2265 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.23 % 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: -0.06 (0.21), residues: 1905 helix: 2.02 (0.20), residues: 740 sheet: -1.74 (0.23), residues: 450 loop : -1.01 (0.25), residues: 715 =============================================================================== Job complete usr+sys time: 2680.35 seconds wall clock time: 50 minutes 12.55 seconds (3012.55 seconds total)