Starting phenix.real_space_refine on Sun Aug 24 18:02:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gb0_29910/08_2025/8gb0_29910.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gb0_29910/08_2025/8gb0_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/cci-nas-00/data/ceres_data/8gb0_29910/08_2025/8gb0_29910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gb0_29910/08_2025/8gb0_29910.map" model { file = "/net/cci-nas-00/data/ceres_data/8gb0_29910/08_2025/8gb0_29910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gb0_29910/08_2025/8gb0_29910.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 10, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} 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: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} 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: {'ASN:plan1': 7, 'ASP:plan': 13, 'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 143 Time building chain proxies: 5.33, per 1000 atoms: 0.25 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: 1.68 Conformation dependent library (CDL) restraints added in 901.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.80 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: 3.92 Time building geometry restraints manager: 2.22 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: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.930 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.510 ------------------------------------------------------------------------------- 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 22062 Z= 0.265 Angle : 0.973 12.424 30116 Z= 0.554 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.015 0.001 ARG C1091 TYR 0.044 0.003 TYR A 495 PHE 0.043 0.003 PHE C 817 TRP 0.026 0.003 TRP A 436 HIS 0.007 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00544 (22026) covalent geometry : angle 0.96982 (30044) SS BOND : bond 0.00480 ( 36) SS BOND : angle 1.93773 ( 72) hydrogen bonds : bond 0.19094 ( 927) hydrogen bonds : angle 9.32493 ( 2592) *********************** 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 : 0.857 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: B 1109 PHE cc_start: 0.9036 (t80) cc_final: 0.8688 (t80) REVERT: B 1119 ASN cc_start: 0.8191 (m110) cc_final: 0.7990 (m-40) REVERT: C 655 TYR cc_start: 0.8341 (t80) cc_final: 0.8132 (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: 0.1500 time to fit residues: 26.7348 Evaluate side-chains 73 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 613 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.053230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.042619 restraints weight = 169164.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.043692 restraints weight = 89812.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.044410 restraints weight = 57967.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.044870 restraints weight = 42367.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.045231 restraints weight = 33955.821| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22062 Z= 0.153 Angle : 0.534 7.129 30116 Z= 0.288 Chirality : 0.043 0.159 3530 Planarity : 0.004 0.052 3886 Dihedral : 4.530 19.707 3034 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.15), residues: 2806 helix: 0.75 (0.19), residues: 676 sheet: -0.19 (0.20), residues: 594 loop : -1.31 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 328 TYR 0.015 0.001 TYR B 265 PHE 0.013 0.001 PHE C 817 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00313 (22026) covalent geometry : angle 0.53213 (30044) SS BOND : bond 0.00347 ( 36) SS BOND : angle 0.98326 ( 72) hydrogen bonds : bond 0.04250 ( 927) hydrogen bonds : angle 6.60220 ( 2592) *********************** 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 108 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 896 ILE cc_start: 0.9007 (pt) cc_final: 0.8744 (pt) REVERT: A 1050 MET cc_start: 0.7756 (mpp) cc_final: 0.7521 (mpp) REVERT: A 1109 PHE cc_start: 0.8054 (t80) cc_final: 0.7618 (t80) REVERT: B 740 MET cc_start: 0.8705 (tpp) cc_final: 0.8042 (tpp) REVERT: B 1050 MET cc_start: 0.7691 (pmm) cc_final: 0.6972 (pmm) REVERT: B 1118 ASP cc_start: 0.9272 (p0) cc_final: 0.9065 (p0) REVERT: C 707 TYR cc_start: 0.8614 (t80) cc_final: 0.8234 (t80) REVERT: C 1050 MET cc_start: 0.8265 (pmm) cc_final: 0.7504 (pmm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1389 time to fit residues: 23.9311 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 : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 0.1980 chunk 223 optimal weight: 7.9990 chunk 142 optimal weight: 0.0000 chunk 63 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 252 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 B1071 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.053271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.042660 restraints weight = 171767.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.043723 restraints weight = 90474.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.044475 restraints weight = 58047.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.044974 restraints weight = 42151.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.045251 restraints weight = 33719.115| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22062 Z= 0.126 Angle : 0.496 6.894 30116 Z= 0.264 Chirality : 0.042 0.141 3530 Planarity : 0.004 0.047 3886 Dihedral : 4.184 19.020 3034 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.15), residues: 2806 helix: 1.45 (0.20), residues: 672 sheet: -0.08 (0.20), residues: 580 loop : -1.19 (0.14), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 328 TYR 0.014 0.001 TYR B 265 PHE 0.025 0.001 PHE A 559 TRP 0.014 0.001 TRP A1102 HIS 0.011 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00259 (22026) covalent geometry : angle 0.49463 (30044) SS BOND : bond 0.00283 ( 36) SS BOND : angle 0.98798 ( 72) hydrogen bonds : bond 0.03975 ( 927) hydrogen bonds : angle 6.10097 ( 2592) *********************** 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 101 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 896 ILE cc_start: 0.9043 (pt) cc_final: 0.8792 (pt) REVERT: A 1109 PHE cc_start: 0.8139 (t80) cc_final: 0.7541 (t80) REVERT: B 740 MET cc_start: 0.8787 (tpp) cc_final: 0.8204 (tpp) REVERT: B 773 GLU cc_start: 0.8262 (tp30) cc_final: 0.7945 (tp30) REVERT: B 776 LYS cc_start: 0.9475 (tttt) cc_final: 0.9207 (tmmt) REVERT: B 1050 MET cc_start: 0.7522 (pmm) cc_final: 0.6956 (pmm) REVERT: B 1109 PHE cc_start: 0.9027 (t80) cc_final: 0.8680 (t80) REVERT: C 707 TYR cc_start: 0.8653 (t80) cc_final: 0.8201 (t80) REVERT: C 1050 MET cc_start: 0.8187 (pmm) cc_final: 0.7424 (pmm) REVERT: C 1071 GLN cc_start: 0.8305 (pt0) cc_final: 0.8062 (mm-40) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1460 time to fit residues: 24.1088 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 : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 80 optimal weight: 7.9990 chunk 115 optimal weight: 0.0470 chunk 221 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 259 optimal weight: 0.4980 chunk 219 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 40.0000 chunk 169 optimal weight: 5.9990 overall best weight: 1.3084 ------------------------------------------------------------------------------- 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 A1010 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN B1071 GLN B1119 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.053370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.042783 restraints weight = 170706.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.043851 restraints weight = 90155.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.044612 restraints weight = 57834.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.045118 restraints weight = 42021.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.045382 restraints weight = 33440.374| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22062 Z= 0.110 Angle : 0.477 7.321 30116 Z= 0.252 Chirality : 0.042 0.159 3530 Planarity : 0.003 0.045 3886 Dihedral : 3.968 18.418 3034 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.04 % Allowed : 2.30 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.15), residues: 2806 helix: 1.79 (0.20), residues: 671 sheet: -0.00 (0.20), residues: 599 loop : -1.13 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 328 TYR 0.014 0.001 TYR B 265 PHE 0.018 0.001 PHE A 559 TRP 0.010 0.001 TRP A1102 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00227 (22026) covalent geometry : angle 0.47450 (30044) SS BOND : bond 0.00251 ( 36) SS BOND : angle 1.11335 ( 72) hydrogen bonds : bond 0.03746 ( 927) hydrogen bonds : angle 5.75220 ( 2592) *********************** 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 101 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 896 ILE cc_start: 0.9016 (pt) cc_final: 0.8788 (pt) REVERT: A 1050 MET cc_start: 0.7962 (mpp) cc_final: 0.7635 (mpp) REVERT: A 1109 PHE cc_start: 0.8109 (t80) cc_final: 0.7500 (t80) REVERT: B 697 MET cc_start: 0.9147 (pmm) cc_final: 0.8929 (pmm) REVERT: B 773 GLU cc_start: 0.8190 (tp30) cc_final: 0.7893 (tp30) REVERT: B 776 LYS cc_start: 0.9466 (tttt) cc_final: 0.9252 (tmmt) REVERT: B 1050 MET cc_start: 0.7462 (pmm) cc_final: 0.6918 (pmm) REVERT: B 1109 PHE cc_start: 0.9012 (t80) cc_final: 0.8688 (t80) REVERT: C 707 TYR cc_start: 0.8697 (t80) cc_final: 0.8319 (t80) REVERT: C 1050 MET cc_start: 0.7982 (pmm) cc_final: 0.7408 (pmm) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.1465 time to fit residues: 24.3840 Evaluate side-chains 65 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 212 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 115 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 231 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 920 GLN B1071 GLN B1119 ASN C 784 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.052320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.041911 restraints weight = 173763.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.042938 restraints weight = 91845.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.043621 restraints weight = 59111.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.044130 restraints weight = 43485.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.044407 restraints weight = 34919.117| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22062 Z= 0.188 Angle : 0.551 7.401 30116 Z= 0.291 Chirality : 0.043 0.170 3530 Planarity : 0.004 0.041 3886 Dihedral : 4.152 18.855 3034 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.15), residues: 2806 helix: 1.74 (0.20), residues: 679 sheet: -0.18 (0.20), residues: 608 loop : -1.09 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 408 TYR 0.015 0.002 TYR C 655 PHE 0.022 0.001 PHE B 906 TRP 0.023 0.001 TRP C 64 HIS 0.009 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00392 (22026) covalent geometry : angle 0.54805 (30044) SS BOND : bond 0.00355 ( 36) SS BOND : angle 1.21412 ( 72) hydrogen bonds : bond 0.04039 ( 927) hydrogen bonds : angle 5.88961 ( 2592) *********************** 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 94 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 PHE cc_start: 0.8256 (t80) cc_final: 0.7477 (t80) REVERT: B 293 LEU cc_start: 0.8251 (mt) cc_final: 0.7978 (mt) REVERT: B 697 MET cc_start: 0.9190 (pmm) cc_final: 0.8816 (pmm) REVERT: B 773 GLU cc_start: 0.8218 (tp30) cc_final: 0.8009 (tp30) REVERT: B 1050 MET cc_start: 0.7733 (pmm) cc_final: 0.6987 (pmm) REVERT: B 1109 PHE cc_start: 0.9026 (t80) cc_final: 0.8654 (t80) REVERT: B 1118 ASP cc_start: 0.9297 (p0) cc_final: 0.9088 (p0) REVERT: C 1050 MET cc_start: 0.8010 (pmm) cc_final: 0.7202 (pmm) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1417 time to fit residues: 21.4878 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 : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 147 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 257 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 265 optimal weight: 8.9990 chunk 129 optimal weight: 40.0000 chunk 114 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A1010 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 920 GLN B1119 ASN C 66 HIS C1071 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.051464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.041243 restraints weight = 175706.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.042237 restraints weight = 94274.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.042921 restraints weight = 61387.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.043388 restraints weight = 45057.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.043661 restraints weight = 36169.243| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22062 Z= 0.260 Angle : 0.635 9.063 30116 Z= 0.339 Chirality : 0.045 0.223 3530 Planarity : 0.004 0.042 3886 Dihedral : 4.605 19.650 3034 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.15), residues: 2806 helix: 1.50 (0.20), residues: 671 sheet: -0.50 (0.20), residues: 620 loop : -1.21 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 403 TYR 0.022 0.002 TYR C 655 PHE 0.023 0.002 PHE A 906 TRP 0.012 0.002 TRP C 64 HIS 0.008 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00545 (22026) covalent geometry : angle 0.63308 (30044) SS BOND : bond 0.00409 ( 36) SS BOND : angle 1.22078 ( 72) hydrogen bonds : bond 0.04470 ( 927) hydrogen bonds : angle 6.21964 ( 2592) *********************** 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 85 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 896 ILE cc_start: 0.9122 (pt) cc_final: 0.8905 (pt) REVERT: A 1109 PHE cc_start: 0.8376 (t80) cc_final: 0.8027 (t80) REVERT: B 697 MET cc_start: 0.9247 (pmm) cc_final: 0.8833 (pmm) REVERT: B 731 MET cc_start: 0.8565 (mtm) cc_final: 0.8261 (mtm) REVERT: B 1050 MET cc_start: 0.7862 (pmm) cc_final: 0.7108 (pmm) REVERT: B 1109 PHE cc_start: 0.9095 (t80) cc_final: 0.8594 (t80) REVERT: C 1050 MET cc_start: 0.8175 (pmm) cc_final: 0.7313 (pmm) REVERT: C 1081 ILE cc_start: 0.9494 (pt) cc_final: 0.9102 (mp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1258 time to fit residues: 18.0641 Evaluate side-chains 60 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 249 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 201 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 920 GLN C1011 GLN C1071 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.052393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.042002 restraints weight = 172500.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.043041 restraints weight = 91727.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.043747 restraints weight = 59486.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.044198 restraints weight = 43414.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.044530 restraints weight = 34920.428| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22062 Z= 0.142 Angle : 0.522 7.928 30116 Z= 0.274 Chirality : 0.043 0.225 3530 Planarity : 0.004 0.045 3886 Dihedral : 4.245 18.224 3034 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.04 % Allowed : 1.42 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.15), residues: 2806 helix: 1.85 (0.20), residues: 673 sheet: -0.40 (0.20), residues: 612 loop : -1.16 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 815 TYR 0.013 0.001 TYR B1067 PHE 0.027 0.001 PHE B 906 TRP 0.010 0.001 TRP C 64 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00300 (22026) covalent geometry : angle 0.51994 (30044) SS BOND : bond 0.00321 ( 36) SS BOND : angle 1.15725 ( 72) hydrogen bonds : bond 0.03892 ( 927) hydrogen bonds : angle 5.86198 ( 2592) *********************** 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 92 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.801 Fit side-chains REVERT: A 1109 PHE cc_start: 0.8296 (t80) cc_final: 0.7797 (t80) REVERT: B 697 MET cc_start: 0.9266 (pmm) cc_final: 0.8994 (pmm) REVERT: B 1050 MET cc_start: 0.7902 (pmm) cc_final: 0.7193 (pmm) REVERT: B 1109 PHE cc_start: 0.9066 (t80) cc_final: 0.8594 (t80) REVERT: C 1050 MET cc_start: 0.8110 (pmm) cc_final: 0.7527 (pmm) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.1158 time to fit residues: 17.5931 Evaluate side-chains 62 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 120 optimal weight: 30.0000 chunk 89 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 254 optimal weight: 0.0030 chunk 214 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 226 optimal weight: 30.0000 chunk 104 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS B 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.051948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.041618 restraints weight = 175652.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.042644 restraints weight = 93274.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.043337 restraints weight = 60457.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.043805 restraints weight = 44237.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.044077 restraints weight = 35497.216| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22062 Z= 0.204 Angle : 0.583 8.431 30116 Z= 0.307 Chirality : 0.044 0.167 3530 Planarity : 0.004 0.044 3886 Dihedral : 4.399 18.333 3034 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.15), residues: 2806 helix: 1.81 (0.20), residues: 666 sheet: -0.54 (0.20), residues: 632 loop : -1.18 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 357 TYR 0.016 0.002 TYR C 655 PHE 0.026 0.002 PHE B 906 TRP 0.008 0.001 TRP C 64 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00431 (22026) covalent geometry : angle 0.57931 (30044) SS BOND : bond 0.00491 ( 36) SS BOND : angle 1.44429 ( 72) hydrogen bonds : bond 0.04149 ( 927) hydrogen bonds : angle 5.96271 ( 2592) *********************** 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 86 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 818 ILE cc_start: 0.9171 (pt) cc_final: 0.8939 (pt) REVERT: A 896 ILE cc_start: 0.9159 (pt) cc_final: 0.8941 (pt) REVERT: A 1109 PHE cc_start: 0.8305 (t80) cc_final: 0.7920 (t80) REVERT: B 697 MET cc_start: 0.9267 (pmm) cc_final: 0.8619 (pmm) REVERT: B 731 MET cc_start: 0.8527 (mtm) cc_final: 0.8228 (mtm) REVERT: B 1050 MET cc_start: 0.7884 (pmm) cc_final: 0.6940 (pmm) REVERT: B 1109 PHE cc_start: 0.9081 (t80) cc_final: 0.8597 (t80) REVERT: C 1050 MET cc_start: 0.7986 (pmm) cc_final: 0.7274 (pmm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1413 time to fit residues: 19.9344 Evaluate side-chains 60 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 67 optimal weight: 0.0470 chunk 258 optimal weight: 0.0170 chunk 138 optimal weight: 0.9990 chunk 271 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 285 optimal weight: 0.0470 chunk 272 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 overall best weight: 0.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 920 GLN C 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.053348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.042839 restraints weight = 167639.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.043921 restraints weight = 88891.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.044599 restraints weight = 57257.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.045120 restraints weight = 42035.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.045420 restraints weight = 33659.791| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22062 Z= 0.095 Angle : 0.508 9.155 30116 Z= 0.261 Chirality : 0.043 0.226 3530 Planarity : 0.004 0.042 3886 Dihedral : 3.966 19.766 3034 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.16), residues: 2806 helix: 2.07 (0.20), residues: 678 sheet: -0.36 (0.20), residues: 629 loop : -0.99 (0.15), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1019 TYR 0.015 0.001 TYR B1067 PHE 0.024 0.001 PHE B 906 TRP 0.011 0.001 TRP A1102 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00197 (22026) covalent geometry : angle 0.50435 (30044) SS BOND : bond 0.00415 ( 36) SS BOND : angle 1.40025 ( 72) hydrogen bonds : bond 0.03585 ( 927) hydrogen bonds : angle 5.48743 ( 2592) *********************** 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 103 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1109 PHE cc_start: 0.8178 (t80) cc_final: 0.7829 (t80) REVERT: B 1050 MET cc_start: 0.7828 (pmm) cc_final: 0.7209 (pmm) REVERT: B 1109 PHE cc_start: 0.8964 (t80) cc_final: 0.8591 (t80) REVERT: C 699 LEU cc_start: 0.8346 (mt) cc_final: 0.7840 (mp) REVERT: C 1050 MET cc_start: 0.7958 (pmm) cc_final: 0.7487 (pmm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1376 time to fit residues: 23.3192 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 : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 263 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 161 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 920 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.052575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.042164 restraints weight = 171529.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.043225 restraints weight = 90700.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.043968 restraints weight = 58177.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.044445 restraints weight = 42255.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.044731 restraints weight = 33726.476| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22062 Z= 0.136 Angle : 0.515 9.007 30116 Z= 0.268 Chirality : 0.043 0.140 3530 Planarity : 0.004 0.041 3886 Dihedral : 3.968 16.770 3034 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.16), residues: 2806 helix: 2.08 (0.20), residues: 680 sheet: -0.33 (0.20), residues: 619 loop : -0.96 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.013 0.001 TYR B1067 PHE 0.023 0.001 PHE B 906 TRP 0.015 0.001 TRP A1102 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00292 (22026) covalent geometry : angle 0.51162 (30044) SS BOND : bond 0.00349 ( 36) SS BOND : angle 1.31142 ( 72) hydrogen bonds : bond 0.03692 ( 927) hydrogen bonds : angle 5.53540 ( 2592) ********************** 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 95 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 PHE cc_start: 0.8235 (t80) cc_final: 0.7833 (t80) REVERT: B 697 MET cc_start: 0.9211 (pmm) cc_final: 0.8892 (pmm) REVERT: B 1050 MET cc_start: 0.7834 (pmm) cc_final: 0.7094 (pmm) REVERT: B 1109 PHE cc_start: 0.9003 (t80) cc_final: 0.8620 (t80) REVERT: C 699 LEU cc_start: 0.8443 (mt) cc_final: 0.7910 (mp) REVERT: C 1050 MET cc_start: 0.7994 (pmm) cc_final: 0.7269 (pmm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1342 time to fit residues: 20.9261 Evaluate side-chains 65 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 63 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 220 optimal weight: 8.9990 chunk 121 optimal weight: 40.0000 chunk 264 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 102 optimal weight: 0.4980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN B 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.052395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.041974 restraints weight = 172011.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.043033 restraints weight = 90942.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.043768 restraints weight = 58394.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.044186 restraints weight = 42422.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.044525 restraints weight = 34458.926| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22062 Z= 0.149 Angle : 0.526 8.710 30116 Z= 0.274 Chirality : 0.043 0.171 3530 Planarity : 0.004 0.043 3886 Dihedral : 4.036 16.939 3034 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.16), residues: 2806 helix: 2.12 (0.20), residues: 674 sheet: -0.29 (0.20), residues: 607 loop : -1.00 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.019 0.001 TYR C 707 PHE 0.025 0.001 PHE B 906 TRP 0.014 0.001 TRP A1102 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00317 (22026) covalent geometry : angle 0.52284 (30044) SS BOND : bond 0.00362 ( 36) SS BOND : angle 1.31287 ( 72) hydrogen bonds : bond 0.03748 ( 927) hydrogen bonds : angle 5.60075 ( 2592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2828.75 seconds wall clock time: 50 minutes 3.33 seconds (3003.33 seconds total)