Starting phenix.real_space_refine on Wed Nov 20 18:35:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb0_29910/11_2024/8gb0_29910.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb0_29910/11_2024/8gb0_29910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb0_29910/11_2024/8gb0_29910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb0_29910/11_2024/8gb0_29910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb0_29910/11_2024/8gb0_29910.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb0_29910/11_2024/8gb0_29910.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.005 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 13797 2.51 5 N 3615 2.21 5 O 4058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21566 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7402 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 48, 'TRANS': 918} Chain breaks: 11 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 6874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 6874 Classifications: {'peptide': 950} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 47, 'TRANS': 902} Chain breaks: 12 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 7290 Classifications: {'peptide': 961} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 48, 'TRANS': 912} Chain breaks: 10 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 13, 'GLU:plan': 13, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 143 Time building chain proxies: 12.55, per 1000 atoms: 0.58 Number of scatterers: 21566 At special positions: 0 Unit cell: (123.9, 130.2, 181.65, 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 96 16.00 O 4058 8.00 N 3615 7.00 C 13797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.01 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.18 Conformation dependent library (CDL) restraints added in 2.9 seconds 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5410 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 45 sheets defined 25.4% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.750A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 747 through 757 removed outlier: 3.705A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.883A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.770A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 966 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.527A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.800A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.690A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.903A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.944A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.555A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 817 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.549A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.054A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.602A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.646A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.657A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.015A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.005A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.720A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.284A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.852A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 968 Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.639A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.017A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.220A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.724A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.857A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 122 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.673A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.476A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.508A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.699A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.753A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.813A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.779A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.801A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 29 through 30 removed outlier: 8.690A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.925A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.223A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.027A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.538A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 5.938A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.810A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC9, first strand: chain 'B' and resid 718 through 721 removed outlier: 6.944A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 724 through 728 Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 807 through 808 removed outlier: 3.996A pdb=" N ARG B 815 " --> pdb=" O ASP B 808 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.510A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.545A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.585A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.195A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 325 removed outlier: 7.512A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.723A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 5.869A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.401A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.559A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.597A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 927 hydrogen bonds defined for protein. 2592 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: 9.64 Time building geometry restraints manager: 6.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3729 1.32 - 1.45: 6755 1.45 - 1.59: 11421 1.59 - 1.72: 1 1.72 - 1.85: 120 Bond restraints: 22026 Sorted by residual: bond pdb=" CA PHE B1109 " pdb=" CB PHE B1109 " ideal model delta sigma weight residual 1.533 1.590 -0.057 1.72e-02 3.38e+03 1.09e+01 bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.537 -0.020 6.70e-03 2.23e+04 8.89e+00 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.335 1.366 -0.032 1.19e-02 7.06e+03 7.11e+00 bond pdb=" C PRO C 225 " pdb=" N LEU C 226 " ideal model delta sigma weight residual 1.332 1.299 0.033 1.29e-02 6.01e+03 6.38e+00 bond pdb=" CD GLN A 774 " pdb=" OE1 GLN A 774 " ideal model delta sigma weight residual 1.231 1.191 0.040 1.90e-02 2.77e+03 4.46e+00 ... (remaining 22021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 29212 2.48 - 4.97: 708 4.97 - 7.45: 89 7.45 - 9.94: 25 9.94 - 12.42: 10 Bond angle restraints: 30044 Sorted by residual: angle pdb=" CA CYS A 760 " pdb=" CB CYS A 760 " pdb=" SG CYS A 760 " ideal model delta sigma weight residual 114.40 126.82 -12.42 2.30e+00 1.89e-01 2.92e+01 angle pdb=" N GLN A 774 " pdb=" CA GLN A 774 " pdb=" CB GLN A 774 " ideal model delta sigma weight residual 110.40 119.11 -8.71 1.63e+00 3.76e-01 2.85e+01 angle pdb=" CA CYS C 760 " pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 114.40 126.61 -12.21 2.30e+00 1.89e-01 2.82e+01 angle pdb=" CA CYS B 760 " pdb=" CB CYS B 760 " pdb=" SG CYS B 760 " ideal model delta sigma weight residual 114.40 126.21 -11.81 2.30e+00 1.89e-01 2.64e+01 angle pdb=" CB ARG C1091 " pdb=" CG ARG C1091 " pdb=" CD ARG C1091 " ideal model delta sigma weight residual 111.30 122.47 -11.17 2.30e+00 1.89e-01 2.36e+01 ... (remaining 30039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 12160 17.90 - 35.80: 796 35.80 - 53.70: 111 53.70 - 71.59: 16 71.59 - 89.49: 10 Dihedral angle restraints: 13093 sinusoidal: 4731 harmonic: 8362 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 175.57 -82.57 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 175.46 -82.46 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.77 66.77 1 1.00e+01 1.00e-02 5.81e+01 ... (remaining 13090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2933 0.072 - 0.143: 540 0.143 - 0.215: 43 0.215 - 0.286: 11 0.286 - 0.358: 3 Chirality restraints: 3530 Sorted by residual: chirality pdb=" CB VAL C 130 " pdb=" CA VAL C 130 " pdb=" CG1 VAL C 130 " pdb=" CG2 VAL C 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CG LEU C 916 " pdb=" CB LEU C 916 " pdb=" CD1 LEU C 916 " pdb=" CD2 LEU C 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILE A 312 " pdb=" CA ILE A 312 " pdb=" CG1 ILE A 312 " pdb=" CG2 ILE A 312 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 3527 not shown) Planarity restraints: 3886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 811 " 0.051 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO A 812 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 812 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 812 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO A 295 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 495 " -0.011 2.00e-02 2.50e+03 2.12e-02 9.01e+00 pdb=" CG TYR A 495 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 495 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 495 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 495 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 495 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 495 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 495 " -0.002 2.00e-02 2.50e+03 ... (remaining 3883 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 6250 2.81 - 3.33: 18053 3.33 - 3.85: 37748 3.85 - 4.38: 41716 4.38 - 4.90: 72199 Nonbonded interactions: 175966 Sorted by model distance: nonbonded pdb=" O ALA C1026 " pdb=" OG SER C1030 " model vdw 2.282 3.040 nonbonded pdb=" O GLN B 804 " pdb=" OG SER B 816 " model vdw 2.289 3.040 nonbonded pdb=" O ALA A 879 " pdb=" OG1 THR A 883 " model vdw 2.292 3.040 nonbonded pdb=" O ALA A1026 " pdb=" OG SER A1030 " model vdw 2.303 3.040 nonbonded pdb=" O ASN A 764 " pdb=" OG1 THR A 768 " model vdw 2.304 3.040 ... (remaining 175961 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 through 345 or (resid 346 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 3 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 381 or (res \ id 382 through 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 or (resid 385 through 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 or (resid 392 through 403 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 404 through 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 through 427 or (resid 428 through 430 and (name N or name CA or name C o \ r name O or name CB )) or resid 431 through 432 or (resid 433 through 442 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 450 through 451 and \ (name N or name CA or name C or name O or name CB )) or (resid 453 and (name N \ or name CA or name C or name O or name CB )) or resid 463 or (resid 464 through \ 466 and (name N or name CA or name C or name O or name CB )) or resid 491 or (re \ sid 492 through 495 and (name N or name CA or name C or name O or name CB )) or \ resid 496 or (resid 497 through 498 and (name N or name CA or name C or name O o \ r name CB )) or resid 499 or (resid 500 through 503 and (name N or name CA or na \ me C or name O or name CB )) or (resid 504 through 506 and (name N or name CA or \ name C or name O or name CB )) or resid 507 or (resid 508 through 515 and (name \ N or name CA or name C or name O or name CB )) or (resid 522 through 524 and (n \ ame N or name CA or name C or name O or name CB )) or resid 525 through 528 or ( \ resid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 \ through 553 or (resid 554 and (name N or name CA or name C or name O or name CB \ )) or resid 555 through 793 or (resid 794 and (name N or name CA or name C or na \ me O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name C o \ r name O or name CB )) or resid 797 through 810 or (resid 811 and (name N or nam \ e CA or name C or name O or name CB )) or resid 812 through 827 or resid 856 thr \ ough 866 or (resid 867 through 868 and (name N or name CA or name C or name O or \ name CB )) or resid 869 through 939 or (resid 940 and (name N or name CA or nam \ e C or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N o \ r name CA or name C or name O or name CB )) or resid 986 through 987 or (resid 9 \ 88 through 989 and (name N or name CA or name C or name O or name CB )) or resid \ 990 through 1141 or (resid 1142 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or \ name CA or name C or name O or name CB )) or resid 1147)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 442 or resid 450 through 451 or resid 453 or resid 46 \ 3 through 501 or resid 503 through 567 or (resid 568 and (name N or name CA or n \ ame C or name O or name CB )) or resid 569 through 570 or (resid 571 and (name N \ or name CA or name C or name O or name CB )) or resid 572 through 581 or (resid \ 582 through 583 and (name N or name CA or name C or name O or name CB )) or res \ id 584 through 585 or (resid 586 and (name N or name CA or name C or name O or n \ ame CB )) or resid 587 through 613 or (resid 614 and (name N or name CA or name \ C or name O or name CB )) or resid 615 through 618 or (resid 619 and (name N or \ name CA or name C or name O or name CB )) or resid 620 through 676 or resid 690 \ through 744 or (resid 745 and (name N or name CA or name C or name O or name CB \ )) or resid 746 through 810 or (resid 811 and (name N or name CA or name C or na \ me O or name CB )) or resid 812 through 827 or resid 856 through 866 or (resid 8 \ 67 through 868 and (name N or name CA or name C or name O or name CB )) or resid \ 869 through 920 or (resid 921 and (name N or name CA or name C or name O or nam \ e CB )) or resid 922 through 939 or (resid 940 and (name N or name CA or name C \ or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N or na \ me CA or name C or name O or name CB )) or resid 986 through 987 or (resid 988 t \ hrough 989 and (name N or name CA or name C or name O or name CB )) or resid 990 \ through 1072 or (resid 1073 and (name N or name CA or name C or name O or name \ CB )) or resid 1074 through 1117 or (resid 1118 and (name N or name CA or name C \ or name O or name CB )) or resid 1119 through 1143 or (resid 1144 through 1146 \ and (name N or name CA or name C or name O or name CB )) or resid 1147)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 thro \ ugh 334 and (name N or name CA or name C or name O or name CB )) or resid 335 th \ rough 344 or (resid 345 through 360 and (name N or name CA or name C or name O o \ r name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 or \ (resid 392 through 403 and (name N or name CA or name C or name O or name CB )) \ or (resid 404 through 411 and (name N or name CA or name C or name O or name CB \ )) or resid 412 through 413 or (resid 414 through 415 and (name N or name CA or \ name C or name O or name CB )) or (resid 416 through 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 or (resid 427 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 432 or ( \ resid 433 through 442 and (name N or name CA or name C or name O or name CB )) o \ r (resid 448 through 449 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 451 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 or (resid 464 through 466 and (name N or name CA or name C or name O or na \ me CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or name C \ or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 through 500 or (resid 501 \ and (name N or name CA or name C or name O or name CB )) or (resid 503 and (name \ N or name CA or name C or name O or name CB )) or (resid 504 through 506 and (n \ ame N or name CA or name C or name O or name CB )) or resid 507 or (resid 508 th \ rough 515 and (name N or name CA or name C or name O or name CB )) or (resid 522 \ through 524 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 25 through 527 or (resid 528 through 529 and (name N or name CA or name C or nam \ e O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA \ or name C or name O or name CB )) or resid 555 through 567 or (resid 568 and (na \ me N or name CA or name C or name O or name CB )) or resid 569 through 570 or (r \ esid 571 and (name N or name CA or name C or name O or name CB )) or resid 572 t \ hrough 581 or (resid 582 through 583 and (name N or name CA or name C or name O \ or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or n \ ame C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 645 or (resid \ 646 through 647 and (name N or name CA or name C or name O or name CB )) or res \ id 648 through 793 or (resid 794 and (name N or name CA or name C or name O or n \ ame CB )) or resid 795 or (resid 796 and (name N or name CA or name C or name O \ or name CB )) or resid 797 through 920 or (resid 921 and (name N or name CA or n \ ame C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1117 or (r \ esid 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 \ through 1141 or (resid 1142 and (name N or name CA or name C or name O or name \ CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or name C \ or name O or name CB )) or resid 1147)) } 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: 3.560 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: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 51.070 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 : 0.005 0.069 22026 Z= 0.352 Angle : 0.970 12.424 30044 Z= 0.553 Chirality : 0.054 0.358 3530 Planarity : 0.008 0.077 3886 Dihedral : 11.942 89.493 7575 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.04 % Allowed : 0.66 % Favored : 99.29 % 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: -1.93 (0.13), residues: 2806 helix: -1.37 (0.16), residues: 658 sheet: -0.28 (0.21), residues: 569 loop : -1.64 (0.13), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 436 HIS 0.007 0.002 HIS A1048 PHE 0.043 0.003 PHE C 817 TYR 0.044 0.003 TYR A 495 ARG 0.015 0.001 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1071 GLN cc_start: 0.8337 (mp-120) cc_final: 0.8024 (mm-40) REVERT: A 1109 PHE cc_start: 0.8075 (t80) cc_final: 0.7448 (t80) REVERT: B 697 MET cc_start: 0.8835 (pmm) cc_final: 0.8557 (pmm) REVERT: B 1050 MET cc_start: 0.7188 (pmm) cc_final: 0.6622 (pmm) REVERT: C 655 TYR cc_start: 0.8341 (t80) cc_final: 0.8131 (t80) REVERT: C 1050 MET cc_start: 0.8196 (pmm) cc_final: 0.7866 (pmm) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.2781 time to fit residues: 49.5315 Evaluate side-chains 72 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 chunk 120 optimal weight: 30.0000 chunk 74 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 224 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 260 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 784 GLN ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 804 GLN B 949 GLN B1002 GLN B1071 GLN C1048 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22026 Z= 0.181 Angle : 0.523 6.822 30044 Z= 0.283 Chirality : 0.043 0.154 3530 Planarity : 0.004 0.053 3886 Dihedral : 4.498 19.866 3034 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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: -0.83 (0.15), residues: 2806 helix: 0.69 (0.19), residues: 675 sheet: -0.16 (0.20), residues: 592 loop : -1.30 (0.14), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS A1088 PHE 0.013 0.001 PHE C 817 TYR 0.014 0.001 TYR B 265 ARG 0.004 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 896 ILE cc_start: 0.9012 (pt) cc_final: 0.8770 (pt) REVERT: A 1050 MET cc_start: 0.7779 (mpp) cc_final: 0.7574 (mpp) REVERT: A 1109 PHE cc_start: 0.8006 (t80) cc_final: 0.7152 (t80) REVERT: B 740 MET cc_start: 0.8402 (tpp) cc_final: 0.7828 (tpp) REVERT: B 1050 MET cc_start: 0.7491 (pmm) cc_final: 0.6848 (pmm) REVERT: B 1109 PHE cc_start: 0.9057 (t80) cc_final: 0.8475 (t80) REVERT: B 1111 GLU cc_start: 0.9012 (pm20) cc_final: 0.8399 (pm20) REVERT: C 707 TYR cc_start: 0.8640 (t80) cc_final: 0.8178 (t80) REVERT: C 1050 MET cc_start: 0.8238 (pmm) cc_final: 0.7442 (pmm) REVERT: C 1113 GLN cc_start: 0.9256 (tp-100) cc_final: 0.9011 (tp-100) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3166 time to fit residues: 56.1830 Evaluate side-chains 69 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 144 optimal weight: 0.4980 chunk 80 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 282 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 209 optimal weight: 9.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 920 GLN B 949 GLN B1071 GLN C 66 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22026 Z= 0.295 Angle : 0.584 6.948 30044 Z= 0.313 Chirality : 0.044 0.145 3530 Planarity : 0.004 0.046 3886 Dihedral : 4.501 19.467 3034 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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: -0.60 (0.15), residues: 2806 helix: 1.32 (0.20), residues: 669 sheet: -0.20 (0.20), residues: 592 loop : -1.29 (0.14), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1102 HIS 0.013 0.002 HIS C1048 PHE 0.026 0.002 PHE A 559 TYR 0.017 0.002 TYR C 655 ARG 0.003 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 896 ILE cc_start: 0.9119 (pt) cc_final: 0.8900 (pt) REVERT: A 900 MET cc_start: 0.8110 (mmp) cc_final: 0.7868 (mmm) REVERT: A 1050 MET cc_start: 0.7937 (mpp) cc_final: 0.7563 (mpp) REVERT: A 1109 PHE cc_start: 0.8234 (t80) cc_final: 0.7885 (t80) REVERT: B 1050 MET cc_start: 0.7580 (pmm) cc_final: 0.6784 (pmm) REVERT: B 1109 PHE cc_start: 0.9067 (t80) cc_final: 0.8503 (t80) REVERT: B 1111 GLU cc_start: 0.8947 (pm20) cc_final: 0.8353 (pm20) REVERT: C 707 TYR cc_start: 0.8816 (t80) cc_final: 0.8344 (t80) REVERT: C 1050 MET cc_start: 0.8179 (pmm) cc_final: 0.7328 (pmm) REVERT: C 1071 GLN cc_start: 0.8753 (pt0) cc_final: 0.8424 (mm-40) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.3269 time to fit residues: 47.3318 Evaluate side-chains 64 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 257 optimal weight: 0.8980 chunk 196 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 124 optimal weight: 0.0370 chunk 175 optimal weight: 4.9990 chunk 262 optimal weight: 0.6980 chunk 277 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 920 GLN B 949 GLN B1071 GLN B1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22026 Z= 0.185 Angle : 0.499 7.056 30044 Z= 0.266 Chirality : 0.043 0.140 3530 Planarity : 0.004 0.044 3886 Dihedral : 4.196 17.903 3034 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.04 % Allowed : 2.26 % Favored : 97.70 % 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: -0.39 (0.15), residues: 2806 helix: 1.70 (0.20), residues: 670 sheet: -0.19 (0.20), residues: 597 loop : -1.21 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1102 HIS 0.009 0.001 HIS C1048 PHE 0.022 0.001 PHE B 906 TYR 0.014 0.001 TYR B 265 ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 896 ILE cc_start: 0.9073 (pt) cc_final: 0.8854 (pt) REVERT: A 1050 MET cc_start: 0.7961 (mpp) cc_final: 0.7698 (mpp) REVERT: A 1109 PHE cc_start: 0.8236 (t80) cc_final: 0.7348 (t80) REVERT: B 1050 MET cc_start: 0.7609 (pmm) cc_final: 0.6821 (pmm) REVERT: B 1109 PHE cc_start: 0.9056 (t80) cc_final: 0.8458 (t80) REVERT: B 1111 GLU cc_start: 0.8965 (pm20) cc_final: 0.8278 (pm20) REVERT: B 1119 ASN cc_start: 0.8474 (m110) cc_final: 0.8233 (m-40) REVERT: C 707 TYR cc_start: 0.8823 (t80) cc_final: 0.8254 (t80) REVERT: C 1050 MET cc_start: 0.8130 (pmm) cc_final: 0.7497 (pmm) outliers start: 1 outliers final: 1 residues processed: 97 average time/residue: 0.3438 time to fit residues: 54.4028 Evaluate side-chains 67 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 231 optimal weight: 0.0270 chunk 157 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 206 optimal weight: 0.0870 chunk 114 optimal weight: 30.0000 chunk 236 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 chunk 249 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN B1071 GLN C1011 GLN C1071 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22026 Z= 0.116 Angle : 0.475 6.654 30044 Z= 0.248 Chirality : 0.042 0.154 3530 Planarity : 0.003 0.043 3886 Dihedral : 3.880 16.912 3034 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -0.15 (0.15), residues: 2806 helix: 1.91 (0.20), residues: 674 sheet: -0.04 (0.20), residues: 601 loop : -1.08 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 64 HIS 0.005 0.001 HIS C1048 PHE 0.014 0.001 PHE B 906 TYR 0.013 0.001 TYR B 265 ARG 0.003 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1050 MET cc_start: 0.8055 (mpp) cc_final: 0.7751 (mpp) REVERT: A 1109 PHE cc_start: 0.8161 (t80) cc_final: 0.7372 (t80) REVERT: B 1050 MET cc_start: 0.7542 (pmm) cc_final: 0.6898 (pmm) REVERT: B 1109 PHE cc_start: 0.9048 (t80) cc_final: 0.8442 (t80) REVERT: B 1111 GLU cc_start: 0.8995 (pm20) cc_final: 0.8300 (pm20) REVERT: C 1050 MET cc_start: 0.7981 (pmm) cc_final: 0.7353 (pmm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3146 time to fit residues: 53.5831 Evaluate side-chains 69 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 93 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 277 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 920 GLN B 949 GLN B 953 ASN B 992 GLN B1071 GLN C 784 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22026 Z= 0.269 Angle : 0.556 7.517 30044 Z= 0.295 Chirality : 0.044 0.206 3530 Planarity : 0.004 0.040 3886 Dihedral : 4.160 17.173 3034 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: -0.25 (0.15), residues: 2806 helix: 1.90 (0.20), residues: 664 sheet: -0.23 (0.20), residues: 612 loop : -1.10 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 64 HIS 0.008 0.001 HIS C1048 PHE 0.023 0.002 PHE B 906 TYR 0.015 0.002 TYR C 655 ARG 0.004 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8028 (mmp) cc_final: 0.7755 (mmm) REVERT: A 1050 MET cc_start: 0.7963 (mpp) cc_final: 0.7762 (mpp) REVERT: A 1071 GLN cc_start: 0.8216 (mp-120) cc_final: 0.7961 (mm-40) REVERT: A 1109 PHE cc_start: 0.8230 (t80) cc_final: 0.7834 (t80) REVERT: B 697 MET cc_start: 0.9274 (pmm) cc_final: 0.8904 (pmm) REVERT: B 1050 MET cc_start: 0.7652 (pmm) cc_final: 0.6929 (pmm) REVERT: B 1109 PHE cc_start: 0.9030 (t80) cc_final: 0.8225 (t80) REVERT: B 1111 GLU cc_start: 0.8938 (pm20) cc_final: 0.7882 (pm20) REVERT: C 1050 MET cc_start: 0.8075 (pmm) cc_final: 0.7173 (pmm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.3481 time to fit residues: 53.2273 Evaluate side-chains 68 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 267 optimal weight: 4.9990 chunk 31 optimal weight: 0.0470 chunk 158 optimal weight: 0.7980 chunk 202 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 233 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 276 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 127 optimal weight: 40.0000 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS A1071 GLN ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN B 949 GLN B 953 ASN B1071 GLN C1071 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22026 Z= 0.163 Angle : 0.494 6.860 30044 Z= 0.258 Chirality : 0.043 0.213 3530 Planarity : 0.003 0.042 3886 Dihedral : 3.993 16.480 3034 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -0.13 (0.16), residues: 2806 helix: 2.01 (0.20), residues: 678 sheet: -0.24 (0.20), residues: 626 loop : -1.02 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 64 HIS 0.005 0.001 HIS C1048 PHE 0.022 0.001 PHE C 800 TYR 0.019 0.001 TYR C 707 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 896 ILE cc_start: 0.9058 (pt) cc_final: 0.8831 (pt) REVERT: A 900 MET cc_start: 0.7896 (mmp) cc_final: 0.7631 (mmm) REVERT: A 1071 GLN cc_start: 0.8254 (mp10) cc_final: 0.8049 (mm-40) REVERT: A 1109 PHE cc_start: 0.8172 (t80) cc_final: 0.7534 (t80) REVERT: B 697 MET cc_start: 0.9234 (pmm) cc_final: 0.8995 (pmm) REVERT: B 1050 MET cc_start: 0.7703 (pmm) cc_final: 0.7066 (pmm) REVERT: B 1109 PHE cc_start: 0.9000 (t80) cc_final: 0.8345 (t80) REVERT: B 1111 GLU cc_start: 0.8955 (pm20) cc_final: 0.8241 (pm20) REVERT: C 1050 MET cc_start: 0.8106 (pmm) cc_final: 0.7411 (pmm) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.3395 time to fit residues: 57.2113 Evaluate side-chains 67 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 171 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 165 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 217 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22026 Z= 0.153 Angle : 0.490 8.430 30044 Z= 0.254 Chirality : 0.043 0.173 3530 Planarity : 0.003 0.040 3886 Dihedral : 3.895 16.444 3034 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -0.04 (0.16), residues: 2806 helix: 2.10 (0.20), residues: 679 sheet: -0.16 (0.20), residues: 623 loop : -0.98 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.004 0.001 HIS C1048 PHE 0.016 0.001 PHE B 906 TYR 0.013 0.001 TYR B1067 ARG 0.003 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7820 (mmp) cc_final: 0.7500 (mmm) REVERT: A 1050 MET cc_start: 0.7940 (mpp) cc_final: 0.7698 (mpp) REVERT: A 1109 PHE cc_start: 0.8143 (t80) cc_final: 0.7694 (t80) REVERT: B 697 MET cc_start: 0.9224 (pmm) cc_final: 0.8976 (pmm) REVERT: B 1050 MET cc_start: 0.7710 (pmm) cc_final: 0.7075 (pmm) REVERT: B 1109 PHE cc_start: 0.9004 (t80) cc_final: 0.8359 (t80) REVERT: B 1111 GLU cc_start: 0.8953 (pm20) cc_final: 0.8222 (pm20) REVERT: C 902 MET cc_start: 0.7981 (mmp) cc_final: 0.7771 (mmp) REVERT: C 1050 MET cc_start: 0.8060 (pmm) cc_final: 0.7373 (pmm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3472 time to fit residues: 56.3663 Evaluate side-chains 66 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 251 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 241 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 264 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 232 optimal weight: 0.8980 chunk 243 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22026 Z= 0.147 Angle : 0.483 7.417 30044 Z= 0.251 Chirality : 0.042 0.179 3530 Planarity : 0.003 0.041 3886 Dihedral : 3.811 16.106 3034 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 0.03 (0.16), residues: 2806 helix: 2.16 (0.20), residues: 683 sheet: -0.15 (0.20), residues: 626 loop : -0.93 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 64 HIS 0.005 0.001 HIS A1048 PHE 0.020 0.001 PHE B 906 TYR 0.018 0.001 TYR C 707 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7822 (mmp) cc_final: 0.7525 (mmm) REVERT: A 1109 PHE cc_start: 0.8135 (t80) cc_final: 0.7684 (t80) REVERT: B 1050 MET cc_start: 0.7661 (pmm) cc_final: 0.7033 (pmm) REVERT: B 1106 GLN cc_start: 0.8770 (pt0) cc_final: 0.8153 (pt0) REVERT: B 1109 PHE cc_start: 0.9009 (t80) cc_final: 0.8072 (t80) REVERT: B 1111 GLU cc_start: 0.8948 (pm20) cc_final: 0.7771 (pm20) REVERT: C 1050 MET cc_start: 0.8033 (pmm) cc_final: 0.7417 (pmm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.3421 time to fit residues: 54.4491 Evaluate side-chains 66 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 256 optimal weight: 0.1980 chunk 169 optimal weight: 2.9990 chunk 272 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 30.0000 chunk 189 optimal weight: 7.9990 chunk 285 optimal weight: 7.9990 chunk 263 optimal weight: 1.9990 chunk 227 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 175 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22026 Z= 0.157 Angle : 0.495 9.330 30044 Z= 0.257 Chirality : 0.043 0.169 3530 Planarity : 0.003 0.040 3886 Dihedral : 3.801 17.281 3034 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 0.03 (0.16), residues: 2806 helix: 2.09 (0.20), residues: 687 sheet: -0.21 (0.20), residues: 637 loop : -0.88 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.005 0.001 HIS A1048 PHE 0.032 0.001 PHE C 898 TYR 0.013 0.001 TYR B1067 ARG 0.003 0.000 ARG B1039 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7834 (mmp) cc_final: 0.7501 (mmm) REVERT: A 1109 PHE cc_start: 0.8144 (t80) cc_final: 0.7701 (t80) REVERT: B 697 MET cc_start: 0.9203 (pmm) cc_final: 0.8990 (pmm) REVERT: B 1050 MET cc_start: 0.7709 (pmm) cc_final: 0.7069 (pmm) REVERT: B 1106 GLN cc_start: 0.8775 (pt0) cc_final: 0.8161 (pt0) REVERT: B 1109 PHE cc_start: 0.9035 (t80) cc_final: 0.8166 (t80) REVERT: B 1111 GLU cc_start: 0.8946 (pm20) cc_final: 0.7766 (pm20) REVERT: C 1050 MET cc_start: 0.8029 (pmm) cc_final: 0.7379 (pmm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3443 time to fit residues: 55.2789 Evaluate side-chains 68 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 139 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 228 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 234 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.052669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.042314 restraints weight = 171326.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.043369 restraints weight = 90814.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.044087 restraints weight = 58609.606| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22026 Z= 0.188 Angle : 0.508 9.080 30044 Z= 0.265 Chirality : 0.043 0.150 3530 Planarity : 0.003 0.041 3886 Dihedral : 3.882 16.364 3034 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 0.01 (0.16), residues: 2806 helix: 2.08 (0.20), residues: 679 sheet: -0.16 (0.20), residues: 622 loop : -0.91 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.005 0.001 HIS A 66 PHE 0.031 0.001 PHE B 906 TYR 0.019 0.001 TYR C 707 ARG 0.003 0.000 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3188.72 seconds wall clock time: 62 minutes 48.88 seconds (3768.88 seconds total)