Starting phenix.real_space_refine on Sun May 25 05:06:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srj_40733/05_2025/8srj_40733.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srj_40733/05_2025/8srj_40733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8srj_40733/05_2025/8srj_40733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srj_40733/05_2025/8srj_40733.map" model { file = "/net/cci-nas-00/data/ceres_data/8srj_40733/05_2025/8srj_40733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srj_40733/05_2025/8srj_40733.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 44 5.16 5 C 16892 2.51 5 N 4676 2.21 5 O 4544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.42s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26156 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 6455 Classifications: {'peptide': 1074} Incomplete info: {'truncation_to_alanine': 636} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1034} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2184 Unresolved non-hydrogen angles: 2729 Unresolved non-hydrogen dihedrals: 1758 Unresolved non-hydrogen chiralities: 189 Planarities with less than four sites: {'GLN:plan1': 34, 'HIS:plan': 16, 'TYR:plan': 6, 'ASN:plan1': 37, 'TRP:plan': 1, 'ASP:plan': 65, 'PHE:plan': 30, 'GLU:plan': 59, 'ARG:plan': 44} Unresolved non-hydrogen planarities: 1209 Chain: "B" Number of atoms: 6455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 6455 Classifications: {'peptide': 1074} Incomplete info: {'truncation_to_alanine': 636} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1034} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2184 Unresolved non-hydrogen angles: 2729 Unresolved non-hydrogen dihedrals: 1758 Unresolved non-hydrogen chiralities: 189 Planarities with less than four sites: {'GLN:plan1': 34, 'HIS:plan': 16, 'TYR:plan': 6, 'ASN:plan1': 37, 'TRP:plan': 1, 'ASP:plan': 65, 'PHE:plan': 30, 'GLU:plan': 59, 'ARG:plan': 44} Unresolved non-hydrogen planarities: 1209 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, D Time building chain proxies: 20.24, per 1000 atoms: 0.77 Number of scatterers: 26156 At special positions: 0 Unit cell: (145, 145, 155.44, 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 44 16.00 O 4544 8.00 N 4676 7.00 C 16892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 997 " - pdb=" SG CYS A1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS C 997 " - pdb=" SG CYS C1006 " distance=2.03 Simple disulfide: pdb=" SG CYS D 997 " - pdb=" SG CYS D1006 " 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: 7.14 Conformation dependent library (CDL) restraints added in 4.1 seconds 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8152 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 12 sheets defined 67.8% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 118 through 135 removed outlier: 3.724A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 187 through 203 removed outlier: 4.116A pdb=" N ALA A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 322 through 336 Processing helix chain 'A' and resid 346 through 358 Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 395 through 406 Processing helix chain 'A' and resid 410 through 422 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.548A pdb=" N CYS A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 458 removed outlier: 3.528A pdb=" N ASN A 450 " --> pdb=" O CYS A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 472 through 476 removed outlier: 4.026A pdb=" N LEU A 476 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 508 Processing helix chain 'A' and resid 513 through 521 removed outlier: 3.738A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.749A pdb=" N SER A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 586 removed outlier: 3.607A pdb=" N TYR A 585 " --> pdb=" O ASP A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 625 through 642 removed outlier: 3.879A pdb=" N THR A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 Processing helix chain 'A' and resid 652 through 680 removed outlier: 4.337A pdb=" N MET A 658 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 692 through 696 removed outlier: 4.091A pdb=" N ASN A 696 " --> pdb=" O ASP A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 715 through 726 Processing helix chain 'A' and resid 727 through 730 Processing helix chain 'A' and resid 735 through 745 Processing helix chain 'A' and resid 788 through 799 Processing helix chain 'A' and resid 801 through 826 Processing helix chain 'A' and resid 833 through 855 Processing helix chain 'A' and resid 859 through 864 Processing helix chain 'A' and resid 866 through 889 removed outlier: 3.611A pdb=" N ARG A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 914 removed outlier: 4.558A pdb=" N PHE A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 906 " --> pdb=" O ILE A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 921 removed outlier: 4.228A pdb=" N ALA A 919 " --> pdb=" O ARG A 916 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 961 removed outlier: 4.936A pdb=" N LYS A 936 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 976 removed outlier: 3.953A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.807A pdb=" N PHE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 996 Processing helix chain 'A' and resid 1013 through 1026 Processing helix chain 'A' and resid 1028 through 1065 removed outlier: 6.460A pdb=" N GLU A1046 " --> pdb=" O MET A1042 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ALA A1047 " --> pdb=" O LYS A1043 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1087 removed outlier: 4.218A pdb=" N LEU A1075 " --> pdb=" O ALA A1071 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU A1076 " --> pdb=" O PRO A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1130 Processing helix chain 'A' and resid 1131 through 1168 removed outlier: 3.559A pdb=" N ALA A1168 " --> pdb=" O LEU A1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 118 through 135 removed outlier: 3.724A pdb=" N ALA B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 187 through 203 removed outlier: 4.116A pdb=" N ALA B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 322 through 336 Processing helix chain 'B' and resid 346 through 358 Processing helix chain 'B' and resid 362 through 377 Processing helix chain 'B' and resid 395 through 406 Processing helix chain 'B' and resid 410 through 422 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 439 through 446 removed outlier: 3.548A pdb=" N CYS B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 458 removed outlier: 3.528A pdb=" N ASN B 450 " --> pdb=" O CYS B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 469 Processing helix chain 'B' and resid 472 through 476 removed outlier: 4.026A pdb=" N LEU B 476 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 508 Processing helix chain 'B' and resid 513 through 521 removed outlier: 3.739A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.749A pdb=" N SER B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 586 removed outlier: 3.608A pdb=" N TYR B 585 " --> pdb=" O ASP B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 Processing helix chain 'B' and resid 612 through 622 Processing helix chain 'B' and resid 625 through 642 removed outlier: 3.879A pdb=" N THR B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 647 Processing helix chain 'B' and resid 652 through 680 removed outlier: 4.338A pdb=" N MET B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN B 659 " --> pdb=" O ARG B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 689 Processing helix chain 'B' and resid 692 through 696 removed outlier: 4.092A pdb=" N ASN B 696 " --> pdb=" O ASP B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 709 through 714 Processing helix chain 'B' and resid 715 through 726 Processing helix chain 'B' and resid 727 through 730 Processing helix chain 'B' and resid 735 through 745 Processing helix chain 'B' and resid 788 through 799 Processing helix chain 'B' and resid 801 through 826 Processing helix chain 'B' and resid 833 through 855 Processing helix chain 'B' and resid 859 through 864 Processing helix chain 'B' and resid 866 through 889 removed outlier: 3.612A pdb=" N ARG B 870 " --> pdb=" O ASP B 866 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 914 removed outlier: 4.558A pdb=" N PHE B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 906 " --> pdb=" O ILE B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 921 removed outlier: 4.228A pdb=" N ALA B 919 " --> pdb=" O ARG B 916 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 961 removed outlier: 4.935A pdb=" N LYS B 936 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 976 removed outlier: 3.952A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.808A pdb=" N PHE B 980 " --> pdb=" O PHE B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 996 Processing helix chain 'B' and resid 1013 through 1026 Processing helix chain 'B' and resid 1028 through 1065 removed outlier: 6.460A pdb=" N GLU B1046 " --> pdb=" O MET B1042 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ALA B1047 " --> pdb=" O LYS B1043 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B1065 " --> pdb=" O ALA B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1087 removed outlier: 4.218A pdb=" N LEU B1075 " --> pdb=" O ALA B1071 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU B1076 " --> pdb=" O PRO B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1102 through 1130 Processing helix chain 'B' and resid 1131 through 1168 removed outlier: 3.560A pdb=" N ALA B1168 " --> pdb=" O LEU B1164 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 118 through 135 removed outlier: 3.723A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 176 Processing helix chain 'C' and resid 187 through 203 removed outlier: 4.116A pdb=" N ALA C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 271 through 286 Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 322 through 336 Processing helix chain 'C' and resid 346 through 358 Processing helix chain 'C' and resid 362 through 377 Processing helix chain 'C' and resid 395 through 406 Processing helix chain 'C' and resid 410 through 422 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 439 through 446 removed outlier: 3.548A pdb=" N CYS C 446 " --> pdb=" O GLU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 458 removed outlier: 3.528A pdb=" N ASN C 450 " --> pdb=" O CYS C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 469 Processing helix chain 'C' and resid 472 through 476 removed outlier: 4.026A pdb=" N LEU C 476 " --> pdb=" O ILE C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 494 through 508 Processing helix chain 'C' and resid 513 through 521 removed outlier: 3.737A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.749A pdb=" N SER C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 586 removed outlier: 3.607A pdb=" N TYR C 585 " --> pdb=" O ASP C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 Processing helix chain 'C' and resid 612 through 622 Processing helix chain 'C' and resid 625 through 642 removed outlier: 3.879A pdb=" N THR C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 647 Processing helix chain 'C' and resid 652 through 680 removed outlier: 4.336A pdb=" N MET C 658 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN C 659 " --> pdb=" O ARG C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 689 Processing helix chain 'C' and resid 692 through 696 removed outlier: 4.091A pdb=" N ASN C 696 " --> pdb=" O ASP C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'C' and resid 715 through 726 Processing helix chain 'C' and resid 727 through 730 Processing helix chain 'C' and resid 735 through 745 Processing helix chain 'C' and resid 788 through 799 Processing helix chain 'C' and resid 801 through 826 Processing helix chain 'C' and resid 833 through 855 Processing helix chain 'C' and resid 859 through 864 Processing helix chain 'C' and resid 866 through 889 removed outlier: 3.612A pdb=" N ARG C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 914 removed outlier: 4.557A pdb=" N PHE C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 906 " --> pdb=" O ILE C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 921 removed outlier: 4.228A pdb=" N ALA C 919 " --> pdb=" O ARG C 916 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 961 removed outlier: 4.936A pdb=" N LYS C 936 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 976 removed outlier: 3.953A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.807A pdb=" N PHE C 980 " --> pdb=" O PHE C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 996 Processing helix chain 'C' and resid 1013 through 1026 Processing helix chain 'C' and resid 1028 through 1065 removed outlier: 6.461A pdb=" N GLU C1046 " --> pdb=" O MET C1042 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ALA C1047 " --> pdb=" O LYS C1043 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1087 removed outlier: 4.219A pdb=" N LEU C1075 " --> pdb=" O ALA C1071 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU C1076 " --> pdb=" O PRO C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1130 Processing helix chain 'C' and resid 1131 through 1168 removed outlier: 3.559A pdb=" N ALA C1168 " --> pdb=" O LEU C1164 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 118 through 135 removed outlier: 3.724A pdb=" N ALA D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 Processing helix chain 'D' and resid 187 through 203 removed outlier: 4.116A pdb=" N ALA D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 271 through 286 Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 322 through 336 Processing helix chain 'D' and resid 346 through 358 Processing helix chain 'D' and resid 362 through 377 Processing helix chain 'D' and resid 395 through 406 Processing helix chain 'D' and resid 410 through 422 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 439 through 446 removed outlier: 3.549A pdb=" N CYS D 446 " --> pdb=" O GLU D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 458 removed outlier: 3.527A pdb=" N ASN D 450 " --> pdb=" O CYS D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 472 through 476 removed outlier: 4.026A pdb=" N LEU D 476 " --> pdb=" O ILE D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 494 through 508 Processing helix chain 'D' and resid 513 through 521 removed outlier: 3.738A pdb=" N ARG D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.749A pdb=" N SER D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 586 removed outlier: 3.607A pdb=" N TYR D 585 " --> pdb=" O ASP D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 Processing helix chain 'D' and resid 612 through 622 Processing helix chain 'D' and resid 625 through 642 removed outlier: 3.879A pdb=" N THR D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 647 Processing helix chain 'D' and resid 652 through 680 removed outlier: 4.337A pdb=" N MET D 658 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN D 659 " --> pdb=" O ARG D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 689 Processing helix chain 'D' and resid 692 through 696 removed outlier: 4.092A pdb=" N ASN D 696 " --> pdb=" O ASP D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 709 through 714 Processing helix chain 'D' and resid 715 through 726 Processing helix chain 'D' and resid 727 through 730 Processing helix chain 'D' and resid 735 through 745 Processing helix chain 'D' and resid 788 through 799 Processing helix chain 'D' and resid 801 through 826 Processing helix chain 'D' and resid 833 through 855 Processing helix chain 'D' and resid 859 through 864 Processing helix chain 'D' and resid 866 through 889 removed outlier: 3.612A pdb=" N ARG D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 914 removed outlier: 4.557A pdb=" N PHE D 905 " --> pdb=" O GLY D 901 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 906 " --> pdb=" O ILE D 902 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 921 removed outlier: 4.228A pdb=" N ALA D 919 " --> pdb=" O ARG D 916 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU D 920 " --> pdb=" O TYR D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 924 through 961 removed outlier: 4.935A pdb=" N LYS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 976 removed outlier: 3.952A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 981 removed outlier: 3.807A pdb=" N PHE D 980 " --> pdb=" O PHE D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 996 Processing helix chain 'D' and resid 1013 through 1026 Processing helix chain 'D' and resid 1028 through 1065 removed outlier: 6.460A pdb=" N GLU D1046 " --> pdb=" O MET D1042 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ALA D1047 " --> pdb=" O LYS D1043 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP D1065 " --> pdb=" O ALA D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1070 through 1087 removed outlier: 4.218A pdb=" N LEU D1075 " --> pdb=" O ALA D1071 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU D1076 " --> pdb=" O PRO D1072 " (cutoff:3.500A) Processing helix chain 'D' and resid 1102 through 1130 Processing helix chain 'D' and resid 1131 through 1168 removed outlier: 3.560A pdb=" N ALA D1168 " --> pdb=" O LEU D1164 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 236 removed outlier: 3.570A pdb=" N LYS A 232 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ARG A 100 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU A 236 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR A 210 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU A 258 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY A 212 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL A 260 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 214 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL A 179 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE A 213 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR A 181 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N THR A 215 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU A 145 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL A 316 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N THR A 292 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL A 318 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 294 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 315 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TYR A 386 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 317 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 60 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'B' and resid 232 through 236 removed outlier: 3.570A pdb=" N LYS B 232 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ARG B 100 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU B 236 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N THR B 210 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU B 258 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY B 212 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL B 260 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 214 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL B 179 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 213 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR B 181 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N THR B 215 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU B 145 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL B 316 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N THR B 292 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B 318 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 294 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 315 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TYR B 386 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL B 317 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 60 Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AA9, first strand: chain 'C' and resid 232 through 236 removed outlier: 3.570A pdb=" N LYS C 232 " --> pdb=" O TRP C 96 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ARG C 100 " --> pdb=" O GLY C 234 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU C 236 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR C 210 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU C 258 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY C 212 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL C 260 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA C 214 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL C 179 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE C 213 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR C 181 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N THR C 215 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU C 145 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL C 316 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N THR C 292 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL C 318 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL C 294 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE C 315 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TYR C 386 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL C 317 " --> pdb=" O TYR C 386 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 60 Processing sheet with id=AB2, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'D' and resid 232 through 236 removed outlier: 3.570A pdb=" N LYS D 232 " --> pdb=" O TRP D 96 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ARG D 100 " --> pdb=" O GLY D 234 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU D 236 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR D 210 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU D 258 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY D 212 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL D 260 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA D 214 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL D 179 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE D 213 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR D 181 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N THR D 215 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU D 145 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL D 316 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N THR D 292 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL D 318 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL D 294 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE D 315 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TYR D 386 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL D 317 " --> pdb=" O TYR D 386 " (cutoff:3.500A) 2072 hydrogen bonds defined for protein. 6096 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.31 Time building geometry restraints manager: 8.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4545 1.32 - 1.45: 6885 1.45 - 1.57: 15242 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 26744 Sorted by residual: bond pdb=" C ALA C1071 " pdb=" N PRO C1072 " ideal model delta sigma weight residual 1.337 1.372 -0.035 1.06e-02 8.90e+03 1.12e+01 bond pdb=" C ALA D1071 " pdb=" N PRO D1072 " ideal model delta sigma weight residual 1.337 1.372 -0.035 1.06e-02 8.90e+03 1.12e+01 bond pdb=" C ALA A1071 " pdb=" N PRO A1072 " ideal model delta sigma weight residual 1.337 1.372 -0.035 1.06e-02 8.90e+03 1.12e+01 bond pdb=" C ALA B1071 " pdb=" N PRO B1072 " ideal model delta sigma weight residual 1.337 1.372 -0.035 1.06e-02 8.90e+03 1.11e+01 bond pdb=" C ASP A 243 " pdb=" N PRO A 244 " ideal model delta sigma weight residual 1.329 1.367 -0.038 1.18e-02 7.18e+03 1.04e+01 ... (remaining 26739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 34825 2.06 - 4.12: 1785 4.12 - 6.17: 363 6.17 - 8.23: 127 8.23 - 10.29: 32 Bond angle restraints: 37132 Sorted by residual: angle pdb=" N ILE B 608 " pdb=" CA ILE B 608 " pdb=" C ILE B 608 " ideal model delta sigma weight residual 111.00 102.65 8.35 1.09e+00 8.42e-01 5.87e+01 angle pdb=" N ILE A 608 " pdb=" CA ILE A 608 " pdb=" C ILE A 608 " ideal model delta sigma weight residual 111.00 102.66 8.34 1.09e+00 8.42e-01 5.85e+01 angle pdb=" N ILE C 608 " pdb=" CA ILE C 608 " pdb=" C ILE C 608 " ideal model delta sigma weight residual 111.00 102.67 8.33 1.09e+00 8.42e-01 5.84e+01 angle pdb=" N ILE D 608 " pdb=" CA ILE D 608 " pdb=" C ILE D 608 " ideal model delta sigma weight residual 111.00 102.68 8.32 1.09e+00 8.42e-01 5.83e+01 angle pdb=" N ILE B 982 " pdb=" CA ILE B 982 " pdb=" C ILE B 982 " ideal model delta sigma weight residual 111.45 104.44 7.01 9.30e-01 1.16e+00 5.69e+01 ... (remaining 37127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.15: 14992 15.15 - 30.30: 628 30.30 - 45.45: 156 45.45 - 60.60: 24 60.60 - 75.75: 16 Dihedral angle restraints: 15816 sinusoidal: 3276 harmonic: 12540 Sorted by residual: dihedral pdb=" CA GLY B 409 " pdb=" C GLY B 409 " pdb=" N LYS B 410 " pdb=" CA LYS B 410 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA GLY D 409 " pdb=" C GLY D 409 " pdb=" N LYS D 410 " pdb=" CA LYS D 410 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA GLY C 409 " pdb=" C GLY C 409 " pdb=" N LYS C 410 " pdb=" CA LYS C 410 " ideal model delta harmonic sigma weight residual 180.00 156.02 23.98 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 15813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3978 0.075 - 0.149: 533 0.149 - 0.224: 48 0.224 - 0.299: 34 0.299 - 0.373: 35 Chirality restraints: 4628 Sorted by residual: chirality pdb=" CA ILE D 982 " pdb=" N ILE D 982 " pdb=" C ILE D 982 " pdb=" CB ILE D 982 " both_signs ideal model delta sigma weight residual False 2.43 2.81 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA ILE A 982 " pdb=" N ILE A 982 " pdb=" C ILE A 982 " pdb=" CB ILE A 982 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA ILE B 982 " pdb=" N ILE B 982 " pdb=" C ILE B 982 " pdb=" CB ILE B 982 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 4625 not shown) Planarity restraints: 4908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 670 " 0.024 2.00e-02 2.50e+03 4.80e-02 2.30e+01 pdb=" C VAL C 670 " -0.083 2.00e-02 2.50e+03 pdb=" O VAL C 670 " 0.031 2.00e-02 2.50e+03 pdb=" N GLY C 671 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 670 " 0.024 2.00e-02 2.50e+03 4.78e-02 2.29e+01 pdb=" C VAL A 670 " -0.083 2.00e-02 2.50e+03 pdb=" O VAL A 670 " 0.031 2.00e-02 2.50e+03 pdb=" N GLY A 671 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 668 " -0.023 2.00e-02 2.50e+03 4.77e-02 2.28e+01 pdb=" C LEU C 668 " 0.082 2.00e-02 2.50e+03 pdb=" O LEU C 668 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA C 669 " -0.028 2.00e-02 2.50e+03 ... (remaining 4905 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 10781 2.96 - 3.44: 26090 3.44 - 3.93: 41168 3.93 - 4.41: 43371 4.41 - 4.90: 72654 Nonbonded interactions: 194064 Sorted by model distance: nonbonded pdb=" OH TYR D 386 " pdb=" O GLY D 392 " model vdw 2.470 3.040 nonbonded pdb=" OH TYR B 386 " pdb=" O GLY B 392 " model vdw 2.470 3.040 nonbonded pdb=" OH TYR C 386 " pdb=" O GLY C 392 " model vdw 2.470 3.040 nonbonded pdb=" OH TYR A 386 " pdb=" O GLY A 392 " model vdw 2.470 3.040 nonbonded pdb=" NH1 ARG D 576 " pdb=" OE1 GLN D 598 " model vdw 2.481 3.120 ... (remaining 194059 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 52 through 1168 or resid 6001 through 6002)) selection = (chain 'B' and (resid 52 through 1168 or resid 1301 through 1302)) selection = (chain 'C' and (resid 52 through 1168 or resid 6001 through 6002)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 65.150 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 26748 Z= 0.423 Angle : 1.121 10.290 37140 Z= 0.672 Chirality : 0.061 0.373 4628 Planarity : 0.011 0.071 4908 Dihedral : 10.697 75.751 7652 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.69 % Allowed : 0.69 % Favored : 98.63 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.59 (0.08), residues: 4272 helix: -4.42 (0.04), residues: 2868 sheet: -1.43 (0.25), residues: 272 loop : -1.31 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D 842 HIS 0.004 0.001 HIS B 457 PHE 0.039 0.004 PHE D1037 TYR 0.030 0.003 TYR B 504 ARG 0.015 0.001 ARG C1123 Details of bonding type rmsd hydrogen bonds : bond 0.15426 ( 2072) hydrogen bonds : angle 8.47438 ( 6096) SS BOND : bond 0.00244 ( 4) SS BOND : angle 0.43092 ( 8) covalent geometry : bond 0.00798 (26744) covalent geometry : angle 1.12130 (37132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 305 time to evaluate : 2.639 Fit side-chains REVERT: A 981 GLN cc_start: 0.9510 (mt0) cc_final: 0.9248 (mt0) REVERT: B 981 GLN cc_start: 0.9504 (mt0) cc_final: 0.9248 (mt0) REVERT: C 981 GLN cc_start: 0.9506 (mt0) cc_final: 0.9247 (mt0) REVERT: D 981 GLN cc_start: 0.9507 (mt0) cc_final: 0.9251 (mt0) outliers start: 8 outliers final: 4 residues processed: 309 average time/residue: 0.2865 time to fit residues: 152.1761 Evaluate side-chains 219 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 215 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain C residue 988 LEU Chi-restraints excluded: chain D residue 988 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 361 optimal weight: 0.0270 chunk 324 optimal weight: 0.1980 chunk 180 optimal weight: 10.0000 chunk 110 optimal weight: 0.0470 chunk 218 optimal weight: 50.0000 chunk 173 optimal weight: 5.9990 chunk 335 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 249 optimal weight: 10.0000 chunk 388 optimal weight: 1.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN B 598 GLN C 598 GLN D 598 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.068025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050843 restraints weight = 144895.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.051954 restraints weight = 67064.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.052644 restraints weight = 39636.415| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.002 0.022 26748 Z= 0.098 Angle : 0.485 8.321 37140 Z= 0.263 Chirality : 0.037 0.131 4628 Planarity : 0.005 0.054 4908 Dihedral : 5.615 59.762 5224 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.37 % Allowed : 9.28 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.11), residues: 4272 helix: -1.32 (0.07), residues: 2856 sheet: -1.22 (0.27), residues: 272 loop : -0.47 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 842 HIS 0.002 0.000 HIS B 660 PHE 0.017 0.001 PHE D 604 TYR 0.012 0.001 TYR B 979 ARG 0.005 0.001 ARG A 617 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 2072) hydrogen bonds : angle 4.60962 ( 6096) SS BOND : bond 0.00040 ( 4) SS BOND : angle 0.42461 ( 8) covalent geometry : bond 0.00190 (26744) covalent geometry : angle 0.48458 (37132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 2.642 Fit side-chains REVERT: A 455 MET cc_start: 0.9283 (mpp) cc_final: 0.9056 (mpp) REVERT: A 875 MET cc_start: 0.9382 (ttp) cc_final: 0.8922 (ttm) REVERT: A 981 GLN cc_start: 0.9478 (mt0) cc_final: 0.9233 (mt0) REVERT: B 455 MET cc_start: 0.9286 (mpp) cc_final: 0.9058 (mpp) REVERT: B 875 MET cc_start: 0.9367 (ttp) cc_final: 0.8896 (ttm) REVERT: B 981 GLN cc_start: 0.9479 (mt0) cc_final: 0.9233 (mt0) REVERT: C 455 MET cc_start: 0.9278 (mpp) cc_final: 0.9021 (mpp) REVERT: C 875 MET cc_start: 0.9367 (ttp) cc_final: 0.8918 (ttm) REVERT: C 981 GLN cc_start: 0.9481 (mt0) cc_final: 0.9233 (mt0) REVERT: D 455 MET cc_start: 0.9276 (mpp) cc_final: 0.9035 (mpp) REVERT: D 875 MET cc_start: 0.9363 (ttp) cc_final: 0.8886 (ttm) REVERT: D 981 GLN cc_start: 0.9478 (mt0) cc_final: 0.9236 (mt0) outliers start: 16 outliers final: 16 residues processed: 224 average time/residue: 0.2533 time to fit residues: 104.4403 Evaluate side-chains 211 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 660 HIS Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 660 HIS Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 660 HIS Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 660 HIS Chi-restraints excluded: chain D residue 817 CYS Chi-restraints excluded: chain D residue 960 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 40 optimal weight: 10.0000 chunk 285 optimal weight: 9.9990 chunk 303 optimal weight: 0.9990 chunk 123 optimal weight: 50.0000 chunk 396 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 371 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.061832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.043591 restraints weight = 149280.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.044563 restraints weight = 69169.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.045181 restraints weight = 41259.169| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26748 Z= 0.209 Angle : 0.557 7.054 37140 Z= 0.307 Chirality : 0.039 0.145 4628 Planarity : 0.004 0.042 4908 Dihedral : 4.701 48.781 5216 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.58 % Allowed : 10.40 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.13), residues: 4272 helix: 1.47 (0.09), residues: 2852 sheet: -1.01 (0.27), residues: 260 loop : 0.02 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 842 HIS 0.005 0.002 HIS A 618 PHE 0.015 0.002 PHE B 879 TYR 0.021 0.002 TYR B1057 ARG 0.005 0.001 ARG A 617 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 2072) hydrogen bonds : angle 4.01118 ( 6096) SS BOND : bond 0.00087 ( 4) SS BOND : angle 0.51579 ( 8) covalent geometry : bond 0.00432 (26744) covalent geometry : angle 0.55700 (37132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 875 MET cc_start: 0.9356 (ttp) cc_final: 0.8991 (ttm) REVERT: D 875 MET cc_start: 0.9356 (ttp) cc_final: 0.8981 (ttm) outliers start: 30 outliers final: 13 residues processed: 221 average time/residue: 0.2505 time to fit residues: 102.8184 Evaluate side-chains 188 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain D residue 817 CYS Chi-restraints excluded: chain D residue 912 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 200 optimal weight: 1.9990 chunk 412 optimal weight: 5.9990 chunk 366 optimal weight: 10.0000 chunk 328 optimal weight: 40.0000 chunk 184 optimal weight: 8.9990 chunk 264 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 273 optimal weight: 20.0000 chunk 205 optimal weight: 6.9990 chunk 353 optimal weight: 50.0000 chunk 313 optimal weight: 30.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 GLN ** B 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.060611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.042900 restraints weight = 152831.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.043304 restraints weight = 75212.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.043485 restraints weight = 44543.335| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26748 Z= 0.227 Angle : 0.528 7.836 37140 Z= 0.289 Chirality : 0.040 0.135 4628 Planarity : 0.004 0.042 4908 Dihedral : 4.725 56.668 5216 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.75 % Allowed : 13.49 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.13), residues: 4272 helix: 2.31 (0.10), residues: 2840 sheet: -0.84 (0.28), residues: 260 loop : 0.34 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 842 HIS 0.003 0.001 HIS D 715 PHE 0.014 0.001 PHE B 879 TYR 0.016 0.002 TYR B1057 ARG 0.003 0.000 ARG D 977 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 2072) hydrogen bonds : angle 3.89898 ( 6096) SS BOND : bond 0.00172 ( 4) SS BOND : angle 0.46381 ( 8) covalent geometry : bond 0.00473 (26744) covalent geometry : angle 0.52840 (37132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 2.992 Fit side-chains REVERT: A 687 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.9011 (tpp) REVERT: A 875 MET cc_start: 0.9366 (ttp) cc_final: 0.9057 (ttm) REVERT: B 687 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.9022 (tpp) REVERT: C 687 MET cc_start: 0.9354 (OUTLIER) cc_final: 0.9020 (tpp) REVERT: C 875 MET cc_start: 0.9354 (ttp) cc_final: 0.9047 (ttm) REVERT: D 687 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.9020 (tpp) outliers start: 32 outliers final: 18 residues processed: 198 average time/residue: 0.2689 time to fit residues: 100.0926 Evaluate side-chains 195 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1121 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 817 CYS Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1121 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 423 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 413 optimal weight: 0.0470 chunk 379 optimal weight: 5.9990 chunk 34 optimal weight: 30.0000 chunk 64 optimal weight: 4.9990 chunk 259 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 340 optimal weight: 0.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.062372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.044971 restraints weight = 152011.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.045257 restraints weight = 71888.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.045681 restraints weight = 41487.684| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26748 Z= 0.140 Angle : 0.453 7.105 37140 Z= 0.243 Chirality : 0.038 0.166 4628 Planarity : 0.003 0.040 4908 Dihedral : 4.384 50.998 5216 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.66 % Allowed : 12.63 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.14), residues: 4272 helix: 2.71 (0.10), residues: 2844 sheet: -0.84 (0.27), residues: 264 loop : 0.66 (0.20), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1052 HIS 0.002 0.001 HIS B 715 PHE 0.014 0.001 PHE A 843 TYR 0.017 0.001 TYR C1057 ARG 0.003 0.000 ARG A 617 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 2072) hydrogen bonds : angle 3.57639 ( 6096) SS BOND : bond 0.00126 ( 4) SS BOND : angle 0.30326 ( 8) covalent geometry : bond 0.00301 (26744) covalent geometry : angle 0.45348 (37132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 2.682 Fit side-chains REVERT: A 687 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8913 (tpp) REVERT: B 687 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8910 (tpp) REVERT: C 687 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8897 (tpp) REVERT: D 687 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8907 (tpp) outliers start: 31 outliers final: 18 residues processed: 208 average time/residue: 0.2559 time to fit residues: 99.3054 Evaluate side-chains 201 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 817 CYS Chi-restraints excluded: chain D residue 912 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 991 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 214 optimal weight: 120.0000 chunk 369 optimal weight: 20.0000 chunk 416 optimal weight: 6.9990 chunk 399 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 226 optimal weight: 0.9990 chunk 24 optimal weight: 30.0000 chunk 243 optimal weight: 7.9990 chunk 199 optimal weight: 2.9990 chunk 353 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 981 GLN ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.061878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.043635 restraints weight = 152724.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.044518 restraints weight = 68855.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.045123 restraints weight = 42435.557| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26748 Z= 0.165 Angle : 0.489 9.520 37140 Z= 0.259 Chirality : 0.038 0.206 4628 Planarity : 0.003 0.038 4908 Dihedral : 4.429 48.676 5216 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.69 % Allowed : 10.57 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.14), residues: 4272 helix: 2.76 (0.10), residues: 2876 sheet: -0.72 (0.27), residues: 264 loop : 0.71 (0.21), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1052 HIS 0.003 0.001 HIS B 82 PHE 0.012 0.001 PHE D 843 TYR 0.018 0.001 TYR C 952 ARG 0.003 0.000 ARG A 617 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 2072) hydrogen bonds : angle 3.62365 ( 6096) SS BOND : bond 0.00114 ( 4) SS BOND : angle 0.32857 ( 8) covalent geometry : bond 0.00352 (26744) covalent geometry : angle 0.48909 (37132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 2.849 Fit side-chains REVERT: A 560 MET cc_start: 0.9223 (mmm) cc_final: 0.8941 (mtt) REVERT: A 687 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8926 (tpp) REVERT: B 560 MET cc_start: 0.9216 (mmm) cc_final: 0.8931 (mtt) REVERT: B 687 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8920 (tpp) REVERT: C 560 MET cc_start: 0.9199 (mmm) cc_final: 0.8920 (mtt) REVERT: C 687 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8911 (tpp) REVERT: D 560 MET cc_start: 0.9199 (mmm) cc_final: 0.8916 (mtt) REVERT: D 687 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8916 (tpp) outliers start: 43 outliers final: 29 residues processed: 208 average time/residue: 0.2793 time to fit residues: 107.9732 Evaluate side-chains 206 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1055 GLN Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 1055 GLN Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1055 GLN Chi-restraints excluded: chain C residue 1121 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 817 CYS Chi-restraints excluded: chain D residue 912 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1055 GLN Chi-restraints excluded: chain D residue 1121 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 120 optimal weight: 50.0000 chunk 49 optimal weight: 4.9990 chunk 311 optimal weight: 0.4980 chunk 1 optimal weight: 50.0000 chunk 342 optimal weight: 50.0000 chunk 69 optimal weight: 40.0000 chunk 70 optimal weight: 0.7980 chunk 422 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 419 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.062260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.044153 restraints weight = 152962.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045120 restraints weight = 69281.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.045681 restraints weight = 40651.965| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26748 Z= 0.118 Angle : 0.442 7.426 37140 Z= 0.234 Chirality : 0.038 0.162 4628 Planarity : 0.003 0.038 4908 Dihedral : 4.253 43.171 5216 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.84 % Allowed : 11.77 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.14), residues: 4272 helix: 2.87 (0.10), residues: 2876 sheet: -0.55 (0.28), residues: 260 loop : 0.78 (0.21), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1052 HIS 0.002 0.001 HIS C 82 PHE 0.012 0.001 PHE D 843 TYR 0.016 0.001 TYR C1057 ARG 0.003 0.000 ARG B 617 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 2072) hydrogen bonds : angle 3.41658 ( 6096) SS BOND : bond 0.00089 ( 4) SS BOND : angle 0.19329 ( 8) covalent geometry : bond 0.00253 (26744) covalent geometry : angle 0.44194 (37132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 2.650 Fit side-chains REVERT: A 456 MET cc_start: 0.8969 (tpp) cc_final: 0.8765 (tpt) REVERT: A 560 MET cc_start: 0.9189 (mmm) cc_final: 0.8860 (mtt) REVERT: A 687 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8869 (tpp) REVERT: B 456 MET cc_start: 0.8966 (tpp) cc_final: 0.8763 (tpt) REVERT: B 560 MET cc_start: 0.9178 (mmm) cc_final: 0.8850 (mtt) REVERT: B 687 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8866 (tpp) REVERT: C 560 MET cc_start: 0.9175 (mmm) cc_final: 0.8841 (mtt) REVERT: C 687 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8861 (tpp) REVERT: D 560 MET cc_start: 0.9171 (mmm) cc_final: 0.8825 (mtt) REVERT: D 687 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8864 (tpp) outliers start: 33 outliers final: 21 residues processed: 203 average time/residue: 0.2586 time to fit residues: 97.3987 Evaluate side-chains 202 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 1055 GLN Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 817 CYS Chi-restraints excluded: chain D residue 912 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 991 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 46 optimal weight: 5.9990 chunk 331 optimal weight: 50.0000 chunk 103 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 196 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 389 optimal weight: 1.9990 chunk 392 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 chunk 17 optimal weight: 50.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.060309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.043313 restraints weight = 156112.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.042828 restraints weight = 81313.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.043142 restraints weight = 55656.409| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 26748 Z= 0.296 Angle : 0.602 7.980 37140 Z= 0.325 Chirality : 0.042 0.189 4628 Planarity : 0.004 0.038 4908 Dihedral : 4.940 56.571 5216 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.09 % Allowed : 12.03 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.13), residues: 4272 helix: 2.60 (0.10), residues: 2876 sheet: -0.59 (0.28), residues: 260 loop : 0.56 (0.20), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C1124 HIS 0.006 0.002 HIS B 682 PHE 0.015 0.002 PHE A1120 TYR 0.017 0.002 TYR A1063 ARG 0.003 0.001 ARG C 576 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 2072) hydrogen bonds : angle 4.10020 ( 6096) SS BOND : bond 0.00106 ( 4) SS BOND : angle 0.85525 ( 8) covalent geometry : bond 0.00622 (26744) covalent geometry : angle 0.60172 (37132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 3.001 Fit side-chains REVERT: A 81 MET cc_start: 0.7174 (ptt) cc_final: 0.6967 (pmm) REVERT: A 687 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.8964 (tpp) REVERT: B 81 MET cc_start: 0.7171 (ptt) cc_final: 0.6964 (pmm) REVERT: B 687 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.8960 (tpp) REVERT: C 687 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.8953 (tpp) REVERT: D 687 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.8953 (tpp) REVERT: D 875 MET cc_start: 0.9293 (ttp) cc_final: 0.8735 (ttt) outliers start: 36 outliers final: 28 residues processed: 200 average time/residue: 0.2887 time to fit residues: 107.2345 Evaluate side-chains 200 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1055 GLN Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 1055 GLN Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1055 GLN Chi-restraints excluded: chain C residue 1121 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 817 CYS Chi-restraints excluded: chain D residue 912 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1055 GLN Chi-restraints excluded: chain D residue 1121 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 399 optimal weight: 0.0470 chunk 313 optimal weight: 40.0000 chunk 128 optimal weight: 50.0000 chunk 55 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 26 optimal weight: 30.0000 chunk 212 optimal weight: 6.9990 chunk 340 optimal weight: 0.0970 chunk 154 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 377 optimal weight: 0.9990 overall best weight: 2.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.061574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.044388 restraints weight = 153651.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.044436 restraints weight = 73224.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.044583 restraints weight = 47646.950| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26748 Z= 0.142 Angle : 0.476 9.536 37140 Z= 0.251 Chirality : 0.038 0.169 4628 Planarity : 0.003 0.038 4908 Dihedral : 4.574 59.391 5216 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.49 % Allowed : 12.46 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.14), residues: 4272 helix: 2.88 (0.10), residues: 2876 sheet: -0.52 (0.28), residues: 260 loop : 0.78 (0.21), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1052 HIS 0.004 0.001 HIS C 903 PHE 0.014 0.001 PHE D 843 TYR 0.014 0.001 TYR C1057 ARG 0.002 0.000 ARG B 617 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 2072) hydrogen bonds : angle 3.55476 ( 6096) SS BOND : bond 0.00050 ( 4) SS BOND : angle 0.16938 ( 8) covalent geometry : bond 0.00306 (26744) covalent geometry : angle 0.47584 (37132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 2.617 Fit side-chains REVERT: A 687 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.8964 (tpp) REVERT: B 687 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8961 (tpp) REVERT: C 81 MET cc_start: 0.6913 (ptt) cc_final: 0.6662 (pmm) REVERT: C 687 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.8957 (tpp) REVERT: D 687 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8956 (tpp) outliers start: 29 outliers final: 21 residues processed: 198 average time/residue: 0.2530 time to fit residues: 93.3330 Evaluate side-chains 200 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 817 CYS Chi-restraints excluded: chain D residue 912 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 991 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 380 optimal weight: 5.9990 chunk 279 optimal weight: 2.9990 chunk 317 optimal weight: 8.9990 chunk 117 optimal weight: 40.0000 chunk 373 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 128 optimal weight: 50.0000 chunk 202 optimal weight: 3.9990 chunk 176 optimal weight: 50.0000 chunk 304 optimal weight: 1.9990 chunk 292 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.061832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.043776 restraints weight = 152787.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.044683 restraints weight = 69094.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.045259 restraints weight = 42223.750| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26748 Z= 0.126 Angle : 0.468 12.551 37140 Z= 0.244 Chirality : 0.038 0.162 4628 Planarity : 0.003 0.038 4908 Dihedral : 4.493 59.772 5216 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.41 % Allowed : 13.06 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.14), residues: 4272 helix: 3.00 (0.10), residues: 2876 sheet: -0.35 (0.28), residues: 260 loop : 0.83 (0.21), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1052 HIS 0.002 0.001 HIS B 80 PHE 0.012 0.001 PHE D 843 TYR 0.018 0.001 TYR A 504 ARG 0.002 0.000 ARG B 617 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 2072) hydrogen bonds : angle 3.42695 ( 6096) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.19966 ( 8) covalent geometry : bond 0.00273 (26744) covalent geometry : angle 0.46775 (37132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 2.642 Fit side-chains REVERT: A 687 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8893 (tpp) REVERT: B 687 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8883 (tpp) REVERT: C 687 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8885 (tpp) REVERT: D 687 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8887 (tpp) REVERT: D 875 MET cc_start: 0.9151 (ttp) cc_final: 0.8738 (ttt) outliers start: 28 outliers final: 23 residues processed: 200 average time/residue: 0.2578 time to fit residues: 96.3263 Evaluate side-chains 207 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1121 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 817 CYS Chi-restraints excluded: chain D residue 912 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 210 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 280 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 171 optimal weight: 7.9990 chunk 234 optimal weight: 50.0000 chunk 86 optimal weight: 4.9990 chunk 299 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS B 80 HIS ** B 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.060508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.043559 restraints weight = 154321.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.043169 restraints weight = 81590.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.043348 restraints weight = 54900.679| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 26748 Z= 0.265 Angle : 0.579 10.025 37140 Z= 0.309 Chirality : 0.041 0.241 4628 Planarity : 0.004 0.037 4908 Dihedral : 4.656 55.155 5216 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.66 % Allowed : 12.89 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.14), residues: 4272 helix: 2.85 (0.10), residues: 2876 sheet: -0.43 (0.29), residues: 260 loop : 0.65 (0.21), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 842 HIS 0.005 0.001 HIS B 682 PHE 0.013 0.001 PHE A1120 TYR 0.037 0.002 TYR A 504 ARG 0.002 0.000 ARG D 617 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 2072) hydrogen bonds : angle 3.89278 ( 6096) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.70368 ( 8) covalent geometry : bond 0.00558 (26744) covalent geometry : angle 0.57932 (37132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6455.10 seconds wall clock time: 113 minutes 10.93 seconds (6790.93 seconds total)