Starting phenix.real_space_refine (version: 1.21rc1) on Sat May 13 02:17:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcl_7082/05_2023/6bcl_7082.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcl_7082/05_2023/6bcl_7082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcl_7082/05_2023/6bcl_7082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcl_7082/05_2023/6bcl_7082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcl_7082/05_2023/6bcl_7082.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcl_7082/05_2023/6bcl_7082.pdb" } resolution = 3.54 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= 0.009 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 136 5.16 5 Na 2 4.78 5 C 19628 2.51 5 N 5340 2.21 5 O 5368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B ARG 637": "NH1" <-> "NH2" Residue "B ARG 644": "NH1" <-> "NH2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B ARG 826": "NH1" <-> "NH2" Residue "B ARG 878": "NH1" <-> "NH2" Residue "B ARG 888": "NH1" <-> "NH2" Residue "B ARG 901": "NH1" <-> "NH2" Residue "B ARG 949": "NH1" <-> "NH2" Residue "B ARG 953": "NH1" <-> "NH2" Residue "B ARG 960": "NH1" <-> "NH2" Residue "B ARG 993": "NH1" <-> "NH2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "B ARG 1118": "NH1" <-> "NH2" Residue "B ARG 1137": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 637": "NH1" <-> "NH2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 826": "NH1" <-> "NH2" Residue "A ARG 878": "NH1" <-> "NH2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 949": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 960": "NH1" <-> "NH2" Residue "A ARG 993": "NH1" <-> "NH2" Residue "A ARG 1063": "NH1" <-> "NH2" Residue "A ARG 1118": "NH1" <-> "NH2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 145": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 249": "NH1" <-> "NH2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ARG 611": "NH1" <-> "NH2" Residue "C ARG 637": "NH1" <-> "NH2" Residue "C ARG 644": "NH1" <-> "NH2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 878": "NH1" <-> "NH2" Residue "C ARG 888": "NH1" <-> "NH2" Residue "C ARG 949": "NH1" <-> "NH2" Residue "C ARG 953": "NH1" <-> "NH2" Residue "C ARG 960": "NH1" <-> "NH2" Residue "C ARG 993": "NH1" <-> "NH2" Residue "C ARG 1063": "NH1" <-> "NH2" Residue "C ARG 1118": "NH1" <-> "NH2" Residue "C ARG 1137": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 611": "NH1" <-> "NH2" Residue "D ARG 637": "NH1" <-> "NH2" Residue "D ARG 644": "NH1" <-> "NH2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D ARG 826": "NH1" <-> "NH2" Residue "D ARG 878": "NH1" <-> "NH2" Residue "D ARG 888": "NH1" <-> "NH2" Residue "D ARG 949": "NH1" <-> "NH2" Residue "D ARG 953": "NH1" <-> "NH2" Residue "D ARG 960": "NH1" <-> "NH2" Residue "D ARG 993": "NH1" <-> "NH2" Residue "D ARG 1063": "NH1" <-> "NH2" Residue "D ARG 1118": "NH1" <-> "NH2" Residue "D ARG 1137": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 30474 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7618 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 37, 'TRANS': 929} Chain breaks: 8 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 78 Chain: "A" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7618 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 37, 'TRANS': 929} Chain breaks: 8 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7618 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 37, 'TRANS': 929} Chain breaks: 8 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7618 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 37, 'TRANS': 929} Chain breaks: 8 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 78 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.09, per 1000 atoms: 0.50 Number of scatterers: 30474 At special positions: 0 Unit cell: (148.73, 148.73, 177.62, 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 136 16.00 Na 2 11.00 O 5368 8.00 N 5340 7.00 C 19628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 989 " - pdb=" SG CYS B1007 " distance=2.03 Simple disulfide: pdb=" SG CYS A 989 " - pdb=" SG CYS A1007 " distance=2.03 Simple disulfide: pdb=" SG CYS C 989 " - pdb=" SG CYS C1007 " distance=2.03 Simple disulfide: pdb=" SG CYS D 989 " - pdb=" SG CYS D1007 " 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 Time building additional restraints: 11.14 Conformation dependent library (CDL) restraints added in 4.5 seconds 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7232 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 12 sheets defined 66.9% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'B' and resid 14 through 19 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 163 through 178 removed outlier: 3.522A pdb=" N SER B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 284 through 295 removed outlier: 4.158A pdb=" N ARG B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 317 removed outlier: 4.354A pdb=" N CYS B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 344 through 356 removed outlier: 3.738A pdb=" N LEU B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 removed outlier: 5.511A pdb=" N GLU B 360 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 362 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.636A pdb=" N ILE B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 404 Processing helix chain 'B' and resid 406 through 415 removed outlier: 4.122A pdb=" N ALA B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.577A pdb=" N LEU B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 449 removed outlier: 3.744A pdb=" N VAL B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 465 removed outlier: 3.916A pdb=" N TYR B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.678A pdb=" N ASN B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 484 " --> pdb=" O GLN B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 558 through 569 removed outlier: 3.630A pdb=" N LEU B 562 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 582 Processing helix chain 'B' and resid 584 through 602 removed outlier: 3.574A pdb=" N LEU B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 Processing helix chain 'B' and resid 634 through 643 removed outlier: 3.563A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 670 through 681 Processing helix chain 'B' and resid 689 through 698 removed outlier: 3.634A pdb=" N LEU B 693 " --> pdb=" O PRO B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 703 removed outlier: 3.651A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 772 Processing helix chain 'B' and resid 774 through 799 Processing helix chain 'B' and resid 807 through 830 removed outlier: 3.562A pdb=" N LEU B 811 " --> pdb=" O SER B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 857 Processing helix chain 'B' and resid 859 through 880 removed outlier: 4.032A pdb=" N THR B 880 " --> pdb=" O GLY B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 900 removed outlier: 4.030A pdb=" N CYS B 892 " --> pdb=" O ARG B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 906 removed outlier: 3.509A pdb=" N PHE B 906 " --> pdb=" O LEU B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 920 removed outlier: 4.012A pdb=" N VAL B 919 " --> pdb=" O LYS B 915 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER B 920 " --> pdb=" O ILE B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 948 removed outlier: 3.717A pdb=" N VAL B 926 " --> pdb=" O MET B 922 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 943 " --> pdb=" O ALA B 939 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 964 Processing helix chain 'B' and resid 964 through 970 removed outlier: 3.682A pdb=" N LEU B 968 " --> pdb=" O TYR B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 984 Processing helix chain 'B' and resid 1012 through 1029 removed outlier: 3.909A pdb=" N VAL B1016 " --> pdb=" O ALA B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1031 through 1067 removed outlier: 5.778A pdb=" N GLY B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN B1049 " --> pdb=" O LYS B1045 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR B1059 " --> pdb=" O LYS B1055 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER B1060 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1089 Processing helix chain 'B' and resid 1113 through 1141 Processing helix chain 'B' and resid 1142 through 1191 removed outlier: 4.486A pdb=" N GLN B1163 " --> pdb=" O LYS B1159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B1164 " --> pdb=" O GLN B1160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP B1168 " --> pdb=" O ILE B1164 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B1169 " --> pdb=" O ARG B1165 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 19 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 163 through 178 removed outlier: 3.522A pdb=" N SER A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 247 through 261 Processing helix chain 'A' and resid 284 through 295 removed outlier: 4.157A pdb=" N ARG A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 removed outlier: 4.354A pdb=" N CYS A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.739A pdb=" N LEU A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 5.510A pdb=" N GLU A 360 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 362 " --> pdb=" O LYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.637A pdb=" N ILE A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 406 through 415 removed outlier: 4.123A pdb=" N ALA A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.576A pdb=" N LEU A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 449 removed outlier: 3.745A pdb=" N VAL A 442 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.915A pdb=" N TYR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.677A pdb=" N ASN A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 484 " --> pdb=" O GLN A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 558 through 569 removed outlier: 3.629A pdb=" N LEU A 562 " --> pdb=" O PRO A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 582 Processing helix chain 'A' and resid 584 through 602 removed outlier: 3.573A pdb=" N LEU A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.562A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 670 through 681 Processing helix chain 'A' and resid 689 through 698 removed outlier: 3.634A pdb=" N LEU A 693 " --> pdb=" O PRO A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.650A pdb=" N ILE A 703 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 772 Processing helix chain 'A' and resid 774 through 799 Processing helix chain 'A' and resid 807 through 830 removed outlier: 3.562A pdb=" N LEU A 811 " --> pdb=" O SER A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 857 Processing helix chain 'A' and resid 859 through 880 removed outlier: 4.032A pdb=" N THR A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 900 removed outlier: 4.030A pdb=" N CYS A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 906 removed outlier: 3.510A pdb=" N PHE A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 920 removed outlier: 4.012A pdb=" N VAL A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER A 920 " --> pdb=" O ILE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 removed outlier: 3.717A pdb=" N VAL A 926 " --> pdb=" O MET A 922 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 943 " --> pdb=" O ALA A 939 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 948 " --> pdb=" O THR A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 964 Processing helix chain 'A' and resid 964 through 970 removed outlier: 3.682A pdb=" N LEU A 968 " --> pdb=" O TYR A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 984 Processing helix chain 'A' and resid 1012 through 1029 removed outlier: 3.910A pdb=" N VAL A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1067 removed outlier: 5.778A pdb=" N GLY A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN A1049 " --> pdb=" O LYS A1045 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR A1059 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER A1060 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1089 Processing helix chain 'A' and resid 1113 through 1141 Processing helix chain 'A' and resid 1142 through 1191 removed outlier: 4.487A pdb=" N GLN A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A1164 " --> pdb=" O GLN A1160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A1168 " --> pdb=" O ILE A1164 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A1169 " --> pdb=" O ARG A1165 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 100 through 109 Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 163 through 178 removed outlier: 3.522A pdb=" N SER C 178 " --> pdb=" O HIS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 247 through 261 Processing helix chain 'C' and resid 284 through 295 removed outlier: 4.157A pdb=" N ARG C 288 " --> pdb=" O LYS C 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 317 removed outlier: 4.354A pdb=" N CYS C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 344 through 356 removed outlier: 3.738A pdb=" N LEU C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 removed outlier: 5.511A pdb=" N GLU C 360 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 362 " --> pdb=" O LYS C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.636A pdb=" N ILE C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 404 Processing helix chain 'C' and resid 406 through 415 removed outlier: 4.124A pdb=" N ALA C 410 " --> pdb=" O ARG C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.577A pdb=" N LEU C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 449 removed outlier: 3.744A pdb=" N VAL C 442 " --> pdb=" O ARG C 438 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 465 removed outlier: 3.917A pdb=" N TYR C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.678A pdb=" N ASN C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 484 " --> pdb=" O GLN C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 558 through 569 removed outlier: 3.629A pdb=" N LEU C 562 " --> pdb=" O PRO C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 582 Processing helix chain 'C' and resid 584 through 602 removed outlier: 3.573A pdb=" N LEU C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 634 Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.562A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 670 through 681 Processing helix chain 'C' and resid 689 through 698 removed outlier: 3.634A pdb=" N LEU C 693 " --> pdb=" O PRO C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 703 removed outlier: 3.651A pdb=" N ILE C 703 " --> pdb=" O PRO C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 772 Processing helix chain 'C' and resid 774 through 799 Processing helix chain 'C' and resid 807 through 830 removed outlier: 3.561A pdb=" N LEU C 811 " --> pdb=" O SER C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 857 Processing helix chain 'C' and resid 859 through 880 removed outlier: 4.032A pdb=" N THR C 880 " --> pdb=" O GLY C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 900 removed outlier: 4.030A pdb=" N CYS C 892 " --> pdb=" O ARG C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 906 removed outlier: 3.520A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 920 removed outlier: 4.012A pdb=" N VAL C 919 " --> pdb=" O LYS C 915 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER C 920 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 948 removed outlier: 3.718A pdb=" N VAL C 926 " --> pdb=" O MET C 922 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA C 943 " --> pdb=" O ALA C 939 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 948 " --> pdb=" O THR C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 964 Processing helix chain 'C' and resid 964 through 970 removed outlier: 3.682A pdb=" N LEU C 968 " --> pdb=" O TYR C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 984 Processing helix chain 'C' and resid 1012 through 1029 removed outlier: 3.911A pdb=" N VAL C1016 " --> pdb=" O ALA C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1067 removed outlier: 5.778A pdb=" N GLY C1048 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN C1049 " --> pdb=" O LYS C1045 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR C1059 " --> pdb=" O LYS C1055 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER C1060 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1089 Processing helix chain 'C' and resid 1113 through 1141 Processing helix chain 'C' and resid 1142 through 1191 removed outlier: 4.487A pdb=" N GLN C1163 " --> pdb=" O LYS C1159 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C1164 " --> pdb=" O GLN C1160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP C1168 " --> pdb=" O ILE C1164 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG C1169 " --> pdb=" O ARG C1165 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C1170 " --> pdb=" O GLU C1166 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 143 through 150 Processing helix chain 'D' and resid 163 through 178 removed outlier: 3.522A pdb=" N SER D 178 " --> pdb=" O HIS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 247 through 261 Processing helix chain 'D' and resid 284 through 295 removed outlier: 4.158A pdb=" N ARG D 288 " --> pdb=" O LYS D 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 317 removed outlier: 4.354A pdb=" N CYS D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 344 through 356 removed outlier: 3.739A pdb=" N LEU D 348 " --> pdb=" O ASP D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 362 removed outlier: 5.511A pdb=" N GLU D 360 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 362 " --> pdb=" O LYS D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.636A pdb=" N ILE D 377 " --> pdb=" O GLU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 406 through 415 removed outlier: 4.124A pdb=" N ALA D 410 " --> pdb=" O ARG D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.578A pdb=" N LEU D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 449 removed outlier: 3.744A pdb=" N VAL D 442 " --> pdb=" O ARG D 438 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 465 removed outlier: 3.916A pdb=" N TYR D 465 " --> pdb=" O LEU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.677A pdb=" N ASN D 476 " --> pdb=" O SER D 472 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA D 484 " --> pdb=" O GLN D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 558 through 569 removed outlier: 3.629A pdb=" N LEU D 562 " --> pdb=" O PRO D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 582 Processing helix chain 'D' and resid 584 through 602 removed outlier: 3.573A pdb=" N LEU D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 Processing helix chain 'D' and resid 634 through 643 removed outlier: 3.562A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 670 through 681 Processing helix chain 'D' and resid 689 through 698 removed outlier: 3.633A pdb=" N LEU D 693 " --> pdb=" O PRO D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 703 removed outlier: 3.651A pdb=" N ILE D 703 " --> pdb=" O PRO D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 772 Processing helix chain 'D' and resid 774 through 799 Processing helix chain 'D' and resid 807 through 830 removed outlier: 3.562A pdb=" N LEU D 811 " --> pdb=" O SER D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 857 Processing helix chain 'D' and resid 859 through 880 removed outlier: 4.032A pdb=" N THR D 880 " --> pdb=" O GLY D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 900 removed outlier: 4.029A pdb=" N CYS D 892 " --> pdb=" O ARG D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 906 Processing helix chain 'D' and resid 912 through 920 removed outlier: 4.012A pdb=" N VAL D 919 " --> pdb=" O LYS D 915 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER D 920 " --> pdb=" O ILE D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 948 removed outlier: 3.717A pdb=" N VAL D 926 " --> pdb=" O MET D 922 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA D 943 " --> pdb=" O ALA D 939 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 948 " --> pdb=" O THR D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 964 Processing helix chain 'D' and resid 964 through 970 removed outlier: 3.682A pdb=" N LEU D 968 " --> pdb=" O TYR D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 980 through 984 Processing helix chain 'D' and resid 1012 through 1029 removed outlier: 3.911A pdb=" N VAL D1016 " --> pdb=" O ALA D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1029 through 1067 removed outlier: 5.778A pdb=" N GLY D1048 " --> pdb=" O SER D1044 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN D1049 " --> pdb=" O LYS D1045 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR D1059 " --> pdb=" O LYS D1055 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER D1060 " --> pdb=" O ALA D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1089 Processing helix chain 'D' and resid 1113 through 1141 Processing helix chain 'D' and resid 1142 through 1191 removed outlier: 4.487A pdb=" N GLN D1163 " --> pdb=" O LYS D1159 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D1164 " --> pdb=" O GLN D1160 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP D1168 " --> pdb=" O ILE D1164 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG D1169 " --> pdb=" O ARG D1165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG D1170 " --> pdb=" O GLU D1166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.525A pdb=" N GLY B 77 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN B 90 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU B 235 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 92 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP B 237 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 94 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 186 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE B 234 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY B 188 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL B 236 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA B 190 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY B 157 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU B 300 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU B 276 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL B 302 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 278 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR B 365 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 301 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 985 through 986 removed outlier: 3.957A pdb=" N ILE B 985 " --> pdb=" O HIS B 998 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA5, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.526A pdb=" N GLY A 77 " --> pdb=" O PHE A 91 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN A 90 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 235 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU A 92 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP A 237 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 94 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 186 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE A 234 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY A 188 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL A 236 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA A 190 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLY A 157 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU A 300 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU A 276 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A 302 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU A 278 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N TYR A 365 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 301 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 985 through 986 removed outlier: 3.956A pdb=" N ILE A 985 " --> pdb=" O HIS A 998 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.526A pdb=" N GLY C 77 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN C 90 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU C 235 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU C 92 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP C 237 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU C 94 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA C 186 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N PHE C 234 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY C 188 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL C 236 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA C 190 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY C 157 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N LEU C 300 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU C 276 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL C 302 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU C 278 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N TYR C 365 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU C 301 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 985 through 986 removed outlier: 3.956A pdb=" N ILE C 985 " --> pdb=" O HIS C 998 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 21 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.526A pdb=" N GLY D 77 " --> pdb=" O PHE D 91 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN D 90 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU D 235 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU D 92 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP D 237 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU D 94 " --> pdb=" O ASP D 237 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA D 186 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N PHE D 234 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY D 188 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL D 236 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA D 190 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY D 157 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU D 300 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU D 276 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL D 302 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU D 278 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR D 365 " --> pdb=" O CYS D 299 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU D 301 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 985 through 986 removed outlier: 3.957A pdb=" N ILE D 985 " --> pdb=" O HIS D 998 " (cutoff:3.500A) 1779 hydrogen bonds defined for protein. 5265 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: 11.11 Time building geometry restraints manager: 12.04 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: 9880 1.34 - 1.46: 7411 1.46 - 1.58: 13649 1.58 - 1.71: 0 1.71 - 1.83: 204 Bond restraints: 31144 Sorted by residual: bond pdb=" C PRO C1073 " pdb=" N PRO C1074 " ideal model delta sigma weight residual 1.337 1.371 -0.034 1.11e-02 8.12e+03 9.52e+00 bond pdb=" C PRO A1073 " pdb=" N PRO A1074 " ideal model delta sigma weight residual 1.337 1.370 -0.034 1.11e-02 8.12e+03 9.20e+00 bond pdb=" C PRO D1073 " pdb=" N PRO D1074 " ideal model delta sigma weight residual 1.337 1.370 -0.034 1.11e-02 8.12e+03 9.13e+00 bond pdb=" C PRO B1073 " pdb=" N PRO B1074 " ideal model delta sigma weight residual 1.337 1.370 -0.033 1.11e-02 8.12e+03 8.88e+00 bond pdb=" C PHE C 340 " pdb=" N PRO C 341 " ideal model delta sigma weight residual 1.334 1.381 -0.048 2.34e-02 1.83e+03 4.13e+00 ... (remaining 31139 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.98: 611 105.98 - 113.00: 16976 113.00 - 120.02: 11803 120.02 - 127.05: 12422 127.05 - 134.07: 420 Bond angle restraints: 42232 Sorted by residual: angle pdb=" N LEU B1030 " pdb=" CA LEU B1030 " pdb=" C LEU B1030 " ideal model delta sigma weight residual 111.36 118.54 -7.18 1.09e+00 8.42e-01 4.34e+01 angle pdb=" N ILE B1029 " pdb=" CA ILE B1029 " pdb=" C ILE B1029 " ideal model delta sigma weight residual 111.67 116.63 -4.96 9.50e-01 1.11e+00 2.72e+01 angle pdb=" N LEU C 948 " pdb=" CA LEU C 948 " pdb=" C LEU C 948 " ideal model delta sigma weight residual 108.41 100.41 8.00 1.63e+00 3.76e-01 2.41e+01 angle pdb=" N LEU A 948 " pdb=" CA LEU A 948 " pdb=" C LEU A 948 " ideal model delta sigma weight residual 108.41 100.44 7.97 1.63e+00 3.76e-01 2.39e+01 angle pdb=" N LEU B 948 " pdb=" CA LEU B 948 " pdb=" C LEU B 948 " ideal model delta sigma weight residual 108.41 100.47 7.94 1.63e+00 3.76e-01 2.37e+01 ... (remaining 42227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 17790 17.64 - 35.28: 588 35.28 - 52.93: 74 52.93 - 70.57: 8 70.57 - 88.21: 20 Dihedral angle restraints: 18480 sinusoidal: 7320 harmonic: 11160 Sorted by residual: dihedral pdb=" CB CYS D 989 " pdb=" SG CYS D 989 " pdb=" SG CYS D1007 " pdb=" CB CYS D1007 " ideal model delta sinusoidal sigma weight residual 93.00 -178.79 -88.21 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS A 989 " pdb=" SG CYS A 989 " pdb=" SG CYS A1007 " pdb=" CB CYS A1007 " ideal model delta sinusoidal sigma weight residual 93.00 -178.82 -88.18 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS C 989 " pdb=" SG CYS C 989 " pdb=" SG CYS C1007 " pdb=" CB CYS C1007 " ideal model delta sinusoidal sigma weight residual 93.00 -178.84 -88.16 1 1.00e+01 1.00e-02 9.29e+01 ... (remaining 18477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3508 0.057 - 0.113: 1152 0.113 - 0.170: 129 0.170 - 0.226: 2 0.226 - 0.283: 5 Chirality restraints: 4796 Sorted by residual: chirality pdb=" CB ILE A 279 " pdb=" CA ILE A 279 " pdb=" CG1 ILE A 279 " pdb=" CG2 ILE A 279 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE D 279 " pdb=" CA ILE D 279 " pdb=" CG1 ILE D 279 " pdb=" CG2 ILE D 279 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB ILE B 279 " pdb=" CA ILE B 279 " pdb=" CG1 ILE B 279 " pdb=" CG2 ILE B 279 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 4793 not shown) Planarity restraints: 5332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 816 " 0.024 2.00e-02 2.50e+03 2.03e-02 1.03e+01 pdb=" CG TRP D 816 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP D 816 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 816 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 816 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP D 816 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 816 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 816 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 816 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 816 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 816 " -0.025 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP A 816 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 816 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 816 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 816 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 816 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 816 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 816 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 816 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 816 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 816 " -0.024 2.00e-02 2.50e+03 2.01e-02 1.01e+01 pdb=" CG TRP B 816 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP B 816 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 816 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 816 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 816 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 816 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 816 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 816 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 816 " -0.002 2.00e-02 2.50e+03 ... (remaining 5329 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 9732 2.84 - 3.35: 27498 3.35 - 3.87: 47502 3.87 - 4.38: 53447 4.38 - 4.90: 92626 Nonbonded interactions: 230805 Sorted by model distance: nonbonded pdb=" O ARG D 354 " pdb=" OG1 THR D 357 " model vdw 2.324 2.440 nonbonded pdb=" O ARG B 354 " pdb=" OG1 THR B 357 " model vdw 2.324 2.440 nonbonded pdb=" O ARG C 354 " pdb=" OG1 THR C 357 " model vdw 2.324 2.440 nonbonded pdb=" O ARG A 354 " pdb=" OG1 THR A 357 " model vdw 2.325 2.440 nonbonded pdb=" O VAL C 506 " pdb=" OG1 THR C 509 " model vdw 2.341 2.440 ... (remaining 230800 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' and resid 12 through 1193) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 0.870 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: 0.030 Extract box with map and model: 6.640 Check model and map are aligned: 0.440 Set scattering table: 0.240 Process input model: 71.970 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 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 : 0.008 0.055 31144 Z= 0.481 Angle : 0.964 10.380 42232 Z= 0.532 Chirality : 0.052 0.283 4796 Planarity : 0.006 0.064 5332 Dihedral : 9.609 76.901 11236 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 0.38 % 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: -4.83 (0.09), residues: 3796 helix: -3.23 (0.06), residues: 2408 sheet: -0.81 (0.37), residues: 208 loop : -3.13 (0.14), residues: 1180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 641 time to evaluate : 3.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 653 average time/residue: 0.5386 time to fit residues: 513.6182 Evaluate side-chains 242 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 3.415 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 5.9990 chunk 291 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 155 optimal weight: 0.9980 chunk 300 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 chunk 348 optimal weight: 0.8980 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN B 229 ASN B 248 ASN B 261 GLN B 436 ASN B 476 ASN ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 861 ASN B1080 HIS A 136 GLN A 229 ASN A 248 ASN A 261 GLN A 436 ASN A 476 ASN ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 HIS C 136 GLN C 229 ASN C 248 ASN C 261 GLN C 436 ASN C 476 ASN C 861 ASN C1080 HIS D 136 GLN D 229 ASN D 261 GLN D 436 ASN D1080 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 31144 Z= 0.320 Angle : 0.696 7.912 42232 Z= 0.359 Chirality : 0.041 0.166 4796 Planarity : 0.005 0.051 5332 Dihedral : 5.175 19.652 4216 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 2.22 % 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: -1.79 (0.12), residues: 3796 helix: -0.42 (0.09), residues: 2440 sheet: -1.06 (0.35), residues: 236 loop : -2.78 (0.17), residues: 1120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 297 time to evaluate : 3.529 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: 71 outliers final: 41 residues processed: 360 average time/residue: 0.4917 time to fit residues: 269.4515 Evaluate side-chains 286 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 245 time to evaluate : 3.620 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.2955 time to fit residues: 26.4287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 290 optimal weight: 20.0000 chunk 237 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 349 optimal weight: 4.9990 chunk 377 optimal weight: 4.9990 chunk 311 optimal weight: 5.9990 chunk 346 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 280 optimal weight: 0.0670 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1013 ASN ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN ** D1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 31144 Z= 0.163 Angle : 0.541 8.477 42232 Z= 0.277 Chirality : 0.037 0.161 4796 Planarity : 0.004 0.049 5332 Dihedral : 4.439 17.413 4216 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.69 % 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: -0.27 (0.13), residues: 3796 helix: 0.95 (0.10), residues: 2484 sheet: -1.01 (0.35), residues: 232 loop : -2.67 (0.17), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 344 time to evaluate : 3.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 4 residues processed: 360 average time/residue: 0.4899 time to fit residues: 270.5391 Evaluate side-chains 250 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 246 time to evaluate : 3.704 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2656 time to fit residues: 6.8207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 6.9990 chunk 262 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 350 optimal weight: 6.9990 chunk 371 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 332 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1047 HIS ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 HIS D1013 ASN D1047 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 31144 Z= 0.332 Angle : 0.642 6.754 42232 Z= 0.328 Chirality : 0.042 0.187 4796 Planarity : 0.004 0.052 5332 Dihedral : 4.605 18.572 4216 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 1.78 % 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: 0.09 (0.14), residues: 3796 helix: 1.26 (0.10), residues: 2484 sheet: -1.02 (0.35), residues: 232 loop : -2.60 (0.17), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 254 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 29 residues processed: 303 average time/residue: 0.4716 time to fit residues: 223.3588 Evaluate side-chains 250 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 221 time to evaluate : 3.554 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2669 time to fit residues: 19.5571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 316 optimal weight: 9.9990 chunk 256 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 333 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN A 351 GLN A1013 ASN C 351 GLN C 861 ASN C1047 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 31144 Z= 0.405 Angle : 0.694 6.679 42232 Z= 0.353 Chirality : 0.043 0.195 4796 Planarity : 0.005 0.052 5332 Dihedral : 4.804 19.182 4216 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer Outliers : 1.03 % 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: 0.10 (0.14), residues: 3796 helix: 1.25 (0.10), residues: 2484 sheet: -1.15 (0.34), residues: 232 loop : -2.53 (0.18), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 232 time to evaluate : 3.369 Fit side-chains outliers start: 33 outliers final: 11 residues processed: 263 average time/residue: 0.4556 time to fit residues: 191.2737 Evaluate side-chains 218 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 207 time to evaluate : 3.494 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2749 time to fit residues: 10.6070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 6.9990 chunk 334 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 217 optimal weight: 30.0000 chunk 91 optimal weight: 4.9990 chunk 371 optimal weight: 0.9980 chunk 308 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 195 optimal weight: 20.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- 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: 0.7846 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 31144 Z= 0.262 Angle : 0.590 7.709 42232 Z= 0.302 Chirality : 0.040 0.201 4796 Planarity : 0.004 0.050 5332 Dihedral : 4.510 17.415 4216 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 1.16 % 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: 0.48 (0.14), residues: 3796 helix: 1.54 (0.11), residues: 2500 sheet: -0.78 (0.35), residues: 208 loop : -2.46 (0.18), residues: 1088 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 244 time to evaluate : 3.670 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 14 residues processed: 270 average time/residue: 0.4698 time to fit residues: 200.5024 Evaluate side-chains 242 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 228 time to evaluate : 3.952 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2836 time to fit residues: 12.4866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 271 optimal weight: 0.4980 chunk 210 optimal weight: 0.8980 chunk 312 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 370 optimal weight: 0.5980 chunk 231 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 170 optimal weight: 0.1980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN B1033 ASN A 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 31144 Z= 0.143 Angle : 0.516 11.832 42232 Z= 0.262 Chirality : 0.037 0.186 4796 Planarity : 0.003 0.048 5332 Dihedral : 4.041 16.680 4216 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 0.59 % 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: 0.95 (0.14), residues: 3796 helix: 1.95 (0.11), residues: 2504 sheet: -0.67 (0.35), residues: 208 loop : -2.41 (0.17), residues: 1084 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 259 time to evaluate : 3.804 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 277 average time/residue: 0.4531 time to fit residues: 200.3774 Evaluate side-chains 231 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 225 time to evaluate : 3.660 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2688 time to fit residues: 8.1977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 221 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 235 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 290 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 31144 Z= 0.224 Angle : 0.581 12.946 42232 Z= 0.292 Chirality : 0.039 0.185 4796 Planarity : 0.004 0.049 5332 Dihedral : 4.106 16.838 4216 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 0.84 % 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: 0.98 (0.14), residues: 3796 helix: 2.01 (0.11), residues: 2472 sheet: -0.64 (0.35), residues: 212 loop : -2.36 (0.18), residues: 1112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 233 time to evaluate : 3.915 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 254 average time/residue: 0.4890 time to fit residues: 195.2578 Evaluate side-chains 237 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 224 time to evaluate : 3.587 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2830 time to fit residues: 11.9252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 323 optimal weight: 10.0000 chunk 344 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 270 optimal weight: 0.9990 chunk 105 optimal weight: 20.0000 chunk 311 optimal weight: 8.9990 chunk 326 optimal weight: 6.9990 chunk 343 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 31144 Z= 0.252 Angle : 0.607 12.986 42232 Z= 0.306 Chirality : 0.040 0.183 4796 Planarity : 0.004 0.048 5332 Dihedral : 4.247 17.399 4216 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 0.34 % 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: 0.88 (0.14), residues: 3796 helix: 1.92 (0.10), residues: 2472 sheet: -0.62 (0.35), residues: 212 loop : -2.37 (0.18), residues: 1112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 232 time to evaluate : 3.677 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 243 average time/residue: 0.4887 time to fit residues: 185.7626 Evaluate side-chains 223 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 218 time to evaluate : 3.572 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2730 time to fit residues: 7.8218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 9.9990 chunk 364 optimal weight: 0.7980 chunk 222 optimal weight: 0.0370 chunk 173 optimal weight: 0.0770 chunk 253 optimal weight: 6.9990 chunk 382 optimal weight: 10.0000 chunk 352 optimal weight: 4.9990 chunk 304 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 overall best weight: 2.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN D1013 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 31144 Z= 0.210 Angle : 0.580 13.044 42232 Z= 0.291 Chirality : 0.039 0.175 4796 Planarity : 0.004 0.048 5332 Dihedral : 4.138 16.985 4216 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.22 % 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: 0.99 (0.14), residues: 3796 helix: 2.00 (0.10), residues: 2480 sheet: -0.60 (0.35), residues: 212 loop : -2.36 (0.18), residues: 1104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 219 time to evaluate : 3.633 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 223 average time/residue: 0.4822 time to fit residues: 170.1181 Evaluate side-chains 220 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 216 time to evaluate : 3.421 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2661 time to fit residues: 6.4337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 280 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 305 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 313 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: