Starting phenix.real_space_refine on Fri Mar 6 00:00:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srj_40733/03_2026/8srj_40733.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srj_40733/03_2026/8srj_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 { model { file = "/net/cci-nas-00/data/ceres_data/8srj_40733/03_2026/8srj_40733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srj_40733/03_2026/8srj_40733.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8srj_40733/03_2026/8srj_40733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srj_40733/03_2026/8srj_40733.map" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26156 Number of models: 1 Model: "" Number of chains: 8 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: {'GLU:plan': 59, 'ASN:plan1': 37, 'ASP:plan': 65, 'ARG:plan': 44, 'GLN:plan1': 34, 'PHE:plan': 30, 'TYR:plan': 6, 'HIS:plan': 16, 'TRP:plan': 1} 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: {'GLU:plan': 59, 'ASN:plan1': 37, 'ASP:plan': 65, 'ARG:plan': 44, 'GLN:plan1': 34, 'PHE:plan': 30, 'TYR:plan': 6, 'HIS:plan': 16, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 1209 Chain: "C" 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: {'GLU:plan': 59, 'ASN:plan1': 37, 'ASP:plan': 65, 'ARG:plan': 44, 'GLN:plan1': 34, 'PHE:plan': 30, 'TYR:plan': 6, 'HIS:plan': 16, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 1209 Chain: "D" 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: {'GLU:plan': 59, 'ASN:plan1': 37, 'ASP:plan': 65, 'ARG:plan': 44, 'GLN:plan1': 34, 'PHE:plan': 30, 'TYR:plan': 6, 'HIS:plan': 16, 'TRP:plan': 1} 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.92, per 1000 atoms: 0.23 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: 2.07 Conformation dependent library (CDL) restraints added in 1.4 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: 0.93 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: 5.65 Time building geometry restraints manager: 2.80 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 6002) selection = (chain 'B' and resid 52 through 1302) selection = (chain 'C' and resid 52 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.610 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.015 0.001 ARG C1123 TYR 0.030 0.003 TYR B 504 PHE 0.039 0.004 PHE D1037 TRP 0.034 0.003 TRP D 842 HIS 0.004 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00798 (26744) covalent geometry : angle 1.12130 (37132) SS BOND : bond 0.00244 ( 4) SS BOND : angle 0.43092 ( 8) hydrogen bonds : bond 0.15426 ( 2072) hydrogen bonds : angle 8.47438 ( 6096) *********************** 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 : 0.898 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: 0.1331 time to fit residues: 71.5291 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 : 0.970 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 50.0000 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.064665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.047974 restraints weight = 148566.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.048070 restraints weight = 66138.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.048428 restraints weight = 43713.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.048641 restraints weight = 34840.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.048641 restraints weight = 30670.111| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 26748 Z= 0.183 Angle : 0.550 7.464 37140 Z= 0.310 Chirality : 0.039 0.142 4628 Planarity : 0.005 0.054 4908 Dihedral : 5.556 53.062 5224 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.55 % Allowed : 10.48 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.11), residues: 4272 helix: -0.86 (0.08), residues: 2864 sheet: -1.21 (0.27), residues: 264 loop : -0.42 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 617 TYR 0.020 0.002 TYR B 979 PHE 0.016 0.001 PHE B 604 TRP 0.014 0.002 TRP B 842 HIS 0.006 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00369 (26744) covalent geometry : angle 0.54979 (37132) SS BOND : bond 0.00118 ( 4) SS BOND : angle 0.30028 ( 8) hydrogen bonds : bond 0.03685 ( 2072) hydrogen bonds : angle 4.48067 ( 6096) *********************** 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 213 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 1.082 Fit side-chains REVERT: A 455 MET cc_start: 0.9296 (mpp) cc_final: 0.9003 (mpp) REVERT: A 875 MET cc_start: 0.9398 (ttp) cc_final: 0.8974 (ttm) REVERT: A 981 GLN cc_start: 0.9505 (mt0) cc_final: 0.9248 (mt0) REVERT: B 455 MET cc_start: 0.9291 (mpp) cc_final: 0.8992 (mpp) REVERT: B 981 GLN cc_start: 0.9482 (mt0) cc_final: 0.9213 (mt0) REVERT: C 455 MET cc_start: 0.9302 (mpp) cc_final: 0.9013 (mpp) REVERT: C 875 MET cc_start: 0.9398 (ttp) cc_final: 0.8980 (ttm) REVERT: C 981 GLN cc_start: 0.9483 (mt0) cc_final: 0.9215 (mt0) REVERT: D 455 MET cc_start: 0.9292 (mpp) cc_final: 0.9005 (mpp) REVERT: D 981 GLN cc_start: 0.9480 (mt0) cc_final: 0.9217 (mt0) outliers start: 18 outliers final: 18 residues processed: 207 average time/residue: 0.1191 time to fit residues: 45.5156 Evaluate side-chains 204 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 825 LEU 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 825 LEU 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 110 optimal weight: 2.9990 chunk 333 optimal weight: 0.0870 chunk 48 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 402 optimal weight: 4.9990 chunk 173 optimal weight: 0.0370 chunk 388 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 404 optimal weight: 0.7980 chunk 297 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 overall best weight: 0.9838 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.065155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.047246 restraints weight = 148504.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.048330 restraints weight = 66241.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048983 restraints weight = 38764.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.049415 restraints weight = 27501.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.049597 restraints weight = 22030.990| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 26748 Z= 0.089 Angle : 0.436 6.139 37140 Z= 0.230 Chirality : 0.037 0.125 4628 Planarity : 0.004 0.038 4908 Dihedral : 4.565 51.622 5216 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.72 % Allowed : 11.08 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.12), residues: 4272 helix: 1.11 (0.09), residues: 2844 sheet: -1.07 (0.27), residues: 272 loop : 0.06 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 617 TYR 0.015 0.001 TYR B1057 PHE 0.014 0.001 PHE A 843 TRP 0.015 0.001 TRP B1052 HIS 0.002 0.000 HIS C 677 Details of bonding type rmsd covalent geometry : bond 0.00178 (26744) covalent geometry : angle 0.43589 (37132) SS BOND : bond 0.00022 ( 4) SS BOND : angle 0.16836 ( 8) hydrogen bonds : bond 0.02912 ( 2072) hydrogen bonds : angle 3.78320 ( 6096) *********************** 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 224 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 875 MET cc_start: 0.9323 (ttp) cc_final: 0.8929 (ttm) REVERT: C 875 MET cc_start: 0.9292 (ttp) cc_final: 0.8870 (ttm) outliers start: 20 outliers final: 15 residues processed: 215 average time/residue: 0.1169 time to fit residues: 46.4513 Evaluate side-chains 206 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 915 MET Chi-restraints excluded: chain D residue 960 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 263 optimal weight: 1.9990 chunk 381 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 133 optimal weight: 20.0000 chunk 216 optimal weight: 50.0000 chunk 116 optimal weight: 50.0000 chunk 137 optimal weight: 40.0000 chunk 237 optimal weight: 7.9990 chunk 135 optimal weight: 0.0070 chunk 218 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.062622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.044297 restraints weight = 150123.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.045279 restraints weight = 69405.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.045904 restraints weight = 42626.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.046343 restraints weight = 30144.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.046437 restraints weight = 24271.363| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26748 Z= 0.138 Angle : 0.461 5.712 37140 Z= 0.250 Chirality : 0.038 0.125 4628 Planarity : 0.003 0.040 4908 Dihedral : 4.355 45.836 5216 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.15 % Allowed : 11.60 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.13), residues: 4272 helix: 2.27 (0.10), residues: 2840 sheet: -0.86 (0.28), residues: 260 loop : 0.32 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 913 TYR 0.022 0.001 TYR D1057 PHE 0.011 0.001 PHE A 879 TRP 0.014 0.001 TRP B1052 HIS 0.003 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00295 (26744) covalent geometry : angle 0.46086 (37132) SS BOND : bond 0.00100 ( 4) SS BOND : angle 0.42769 ( 8) hydrogen bonds : bond 0.03368 ( 2072) hydrogen bonds : angle 3.57960 ( 6096) *********************** 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: 25 poor density : 185 time to evaluate : 0.867 Fit side-chains REVERT: A 560 MET cc_start: 0.9318 (mmm) cc_final: 0.8871 (mmm) REVERT: A 687 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8855 (tpp) REVERT: A 875 MET cc_start: 0.9382 (ttp) cc_final: 0.8970 (ttm) REVERT: B 560 MET cc_start: 0.9388 (mmm) cc_final: 0.8870 (mmm) REVERT: B 687 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8846 (tpp) REVERT: C 560 MET cc_start: 0.9386 (mmm) cc_final: 0.8874 (mmm) REVERT: C 687 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8813 (tpp) REVERT: C 875 MET cc_start: 0.9374 (ttp) cc_final: 0.8955 (ttm) REVERT: D 560 MET cc_start: 0.9381 (mmm) cc_final: 0.8860 (mmm) REVERT: D 687 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8839 (tpp) outliers start: 25 outliers final: 10 residues processed: 198 average time/residue: 0.1173 time to fit residues: 43.4953 Evaluate side-chains 190 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 912 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1055 GLN Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 817 CYS 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 D residue 687 MET Chi-restraints excluded: chain D residue 817 CYS Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 405 optimal weight: 4.9990 chunk 109 optimal weight: 50.0000 chunk 164 optimal weight: 3.9990 chunk 290 optimal weight: 10.0000 chunk 328 optimal weight: 6.9990 chunk 391 optimal weight: 0.7980 chunk 313 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.061647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.043599 restraints weight = 150936.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.044580 restraints weight = 68410.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.045084 restraints weight = 40403.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.045518 restraints weight = 30391.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.045742 restraints weight = 24351.450| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26748 Z= 0.148 Angle : 0.460 8.378 37140 Z= 0.247 Chirality : 0.038 0.162 4628 Planarity : 0.003 0.040 4908 Dihedral : 4.230 50.428 5216 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.32 % Allowed : 12.03 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.13), residues: 4272 helix: 2.60 (0.10), residues: 2872 sheet: -0.68 (0.28), residues: 260 loop : 0.52 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 617 TYR 0.016 0.001 TYR A1057 PHE 0.012 0.001 PHE D 843 TRP 0.013 0.001 TRP B1052 HIS 0.002 0.001 HIS C 715 Details of bonding type rmsd covalent geometry : bond 0.00314 (26744) covalent geometry : angle 0.46010 (37132) SS BOND : bond 0.00071 ( 4) SS BOND : angle 0.30362 ( 8) hydrogen bonds : bond 0.03204 ( 2072) hydrogen bonds : angle 3.51877 ( 6096) *********************** 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 217 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.891 Fit side-chains REVERT: A 560 MET cc_start: 0.9393 (mmm) cc_final: 0.8931 (mmm) REVERT: A 687 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8894 (tpp) REVERT: B 560 MET cc_start: 0.9440 (mmm) cc_final: 0.8941 (mmm) REVERT: B 687 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8888 (tpp) REVERT: C 560 MET cc_start: 0.9436 (mmm) cc_final: 0.8940 (mmm) REVERT: C 687 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8878 (tpp) REVERT: D 560 MET cc_start: 0.9434 (mmm) cc_final: 0.8938 (mmm) REVERT: D 687 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8880 (tpp) outliers start: 27 outliers final: 15 residues processed: 199 average time/residue: 0.1126 time to fit residues: 41.8142 Evaluate side-chains 203 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1055 GLN Chi-restraints excluded: chain B residue 687 MET 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 825 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1055 GLN Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1055 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 410 optimal weight: 1.9990 chunk 231 optimal weight: 40.0000 chunk 366 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 405 optimal weight: 4.9990 chunk 395 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 189 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.062641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.045183 restraints weight = 152834.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.045601 restraints weight = 73763.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.045764 restraints weight = 41392.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.045831 restraints weight = 40692.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.045930 restraints weight = 34905.869| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26748 Z= 0.131 Angle : 0.445 7.746 37140 Z= 0.236 Chirality : 0.038 0.229 4628 Planarity : 0.003 0.039 4908 Dihedral : 4.221 53.757 5216 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.26 % Allowed : 10.65 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.14), residues: 4272 helix: 2.92 (0.10), residues: 2848 sheet: -0.69 (0.28), residues: 264 loop : 0.85 (0.20), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 617 TYR 0.017 0.001 TYR D1057 PHE 0.013 0.001 PHE D 843 TRP 0.013 0.001 TRP A1052 HIS 0.002 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00283 (26744) covalent geometry : angle 0.44535 (37132) SS BOND : bond 0.00078 ( 4) SS BOND : angle 0.33251 ( 8) hydrogen bonds : bond 0.03142 ( 2072) hydrogen bonds : angle 3.41812 ( 6096) *********************** 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 226 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.811 Fit side-chains REVERT: A 560 MET cc_start: 0.9364 (mmm) cc_final: 0.9002 (mmm) REVERT: A 687 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8863 (tpp) REVERT: B 560 MET cc_start: 0.9435 (mmm) cc_final: 0.8994 (mmm) REVERT: B 687 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8853 (tpp) REVERT: C 560 MET cc_start: 0.9416 (mmm) cc_final: 0.8999 (mmm) REVERT: C 687 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8832 (tpp) REVERT: D 560 MET cc_start: 0.9433 (mmm) cc_final: 0.8991 (mmm) REVERT: D 687 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8853 (tpp) outliers start: 38 outliers final: 15 residues processed: 215 average time/residue: 0.1189 time to fit residues: 47.2917 Evaluate side-chains 201 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 912 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 912 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 912 LEU Chi-restraints excluded: chain C residue 960 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 825 LEU Chi-restraints excluded: chain D residue 960 LEU 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 235 optimal weight: 50.0000 chunk 182 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 209 optimal weight: 0.9990 chunk 244 optimal weight: 50.0000 chunk 167 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 chunk 153 optimal weight: 0.5980 chunk 352 optimal weight: 50.0000 chunk 80 optimal weight: 2.9990 chunk 405 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.062195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.044077 restraints weight = 153547.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.045036 restraints weight = 68878.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.045591 restraints weight = 40946.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.046003 restraints weight = 30255.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.046143 restraints weight = 24490.907| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26748 Z= 0.150 Angle : 0.467 6.973 37140 Z= 0.247 Chirality : 0.038 0.159 4628 Planarity : 0.003 0.039 4908 Dihedral : 4.249 57.929 5216 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.41 % Allowed : 10.65 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.26 (0.14), residues: 4272 helix: 2.94 (0.10), residues: 2876 sheet: -0.51 (0.28), residues: 268 loop : 0.81 (0.21), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 617 TYR 0.022 0.001 TYR D 952 PHE 0.011 0.001 PHE A1120 TRP 0.013 0.001 TRP C1052 HIS 0.004 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00320 (26744) covalent geometry : angle 0.46727 (37132) SS BOND : bond 0.00095 ( 4) SS BOND : angle 0.34064 ( 8) hydrogen bonds : bond 0.03238 ( 2072) hydrogen bonds : angle 3.47762 ( 6096) *********************** 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 213 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.865 Fit side-chains REVERT: A 560 MET cc_start: 0.9393 (mmm) cc_final: 0.8967 (mmm) REVERT: A 687 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8841 (tpp) REVERT: B 560 MET cc_start: 0.9476 (mmm) cc_final: 0.9014 (mmm) REVERT: B 687 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8835 (tpp) REVERT: C 560 MET cc_start: 0.9467 (mmm) cc_final: 0.9025 (mmm) REVERT: C 687 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8829 (tpp) REVERT: D 560 MET cc_start: 0.9479 (mmm) cc_final: 0.9027 (mmm) REVERT: D 687 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8824 (tpp) outliers start: 28 outliers final: 22 residues processed: 201 average time/residue: 0.1165 time to fit residues: 43.4904 Evaluate side-chains 208 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 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 912 LEU 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 960 LEU 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 825 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1055 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 71 optimal weight: 8.9990 chunk 69 optimal weight: 50.0000 chunk 340 optimal weight: 0.1980 chunk 394 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 385 optimal weight: 7.9990 chunk 398 optimal weight: 3.9990 chunk 127 optimal weight: 50.0000 chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 overall best weight: 3.4388 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.061793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.043638 restraints weight = 152489.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.044524 restraints weight = 69022.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.044908 restraints weight = 42275.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.045397 restraints weight = 33002.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.045693 restraints weight = 26059.046| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4393 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= 0.163 Angle : 0.481 9.211 37140 Z= 0.254 Chirality : 0.039 0.188 4628 Planarity : 0.003 0.038 4908 Dihedral : 4.277 58.273 5216 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.01 % Allowed : 10.74 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.37 (0.14), residues: 4272 helix: 3.01 (0.10), residues: 2876 sheet: -0.41 (0.28), residues: 268 loop : 0.88 (0.21), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 617 TYR 0.018 0.001 TYR D 952 PHE 0.012 0.001 PHE D 843 TRP 0.013 0.001 TRP D1052 HIS 0.002 0.001 HIS D 682 Details of bonding type rmsd covalent geometry : bond 0.00346 (26744) covalent geometry : angle 0.48066 (37132) SS BOND : bond 0.00099 ( 4) SS BOND : angle 0.41373 ( 8) hydrogen bonds : bond 0.03343 ( 2072) hydrogen bonds : angle 3.49288 ( 6096) *********************** 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 222 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.918 Fit side-chains REVERT: A 560 MET cc_start: 0.9433 (mmm) cc_final: 0.9026 (mmm) REVERT: A 687 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8847 (tpp) REVERT: B 560 MET cc_start: 0.9474 (mmm) cc_final: 0.9039 (mmm) REVERT: B 687 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8851 (tpp) REVERT: C 560 MET cc_start: 0.9467 (mmm) cc_final: 0.9035 (mmm) REVERT: C 687 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8839 (tpp) REVERT: D 560 MET cc_start: 0.9468 (mmm) cc_final: 0.9037 (mmm) REVERT: D 687 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8846 (tpp) REVERT: D 875 MET cc_start: 0.9166 (ttp) cc_final: 0.8537 (ttt) outliers start: 35 outliers final: 25 residues processed: 210 average time/residue: 0.1162 time to fit residues: 45.5100 Evaluate side-chains 216 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 912 LEU 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 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 960 LEU 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 825 LEU Chi-restraints excluded: chain D residue 912 LEU Chi-restraints excluded: chain D residue 960 LEU 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 210 optimal weight: 10.0000 chunk 69 optimal weight: 30.0000 chunk 100 optimal weight: 50.0000 chunk 323 optimal weight: 50.0000 chunk 18 optimal weight: 50.0000 chunk 113 optimal weight: 0.0050 chunk 319 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 216 optimal weight: 50.0000 chunk 63 optimal weight: 10.0000 chunk 408 optimal weight: 4.9990 overall best weight: 5.0004 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.060985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.044040 restraints weight = 154612.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.043581 restraints weight = 80935.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.043879 restraints weight = 53839.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.043994 restraints weight = 41486.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.044068 restraints weight = 37819.538| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26748 Z= 0.231 Angle : 0.547 15.647 37140 Z= 0.291 Chirality : 0.041 0.236 4628 Planarity : 0.003 0.036 4908 Dihedral : 4.491 56.226 5216 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.84 % Allowed : 10.57 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.14), residues: 4272 helix: 2.90 (0.10), residues: 2876 sheet: -0.36 (0.28), residues: 268 loop : 0.78 (0.21), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 617 TYR 0.022 0.002 TYR D 952 PHE 0.015 0.001 PHE B 879 TRP 0.013 0.002 TRP D1052 HIS 0.005 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00487 (26744) covalent geometry : angle 0.54700 (37132) SS BOND : bond 0.00064 ( 4) SS BOND : angle 0.63440 ( 8) hydrogen bonds : bond 0.03833 ( 2072) hydrogen bonds : angle 3.82110 ( 6096) *********************** 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 209 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.871 Fit side-chains REVERT: A 456 MET cc_start: 0.9032 (tpp) cc_final: 0.8832 (tpt) REVERT: A 687 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8936 (tpp) REVERT: B 456 MET cc_start: 0.9022 (tpp) cc_final: 0.8819 (tpt) REVERT: B 687 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.8941 (tpp) REVERT: C 456 MET cc_start: 0.9034 (tpp) cc_final: 0.8832 (tpt) REVERT: C 687 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8925 (tpp) REVERT: D 456 MET cc_start: 0.9030 (tpp) cc_final: 0.8827 (tpt) REVERT: D 687 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.8932 (tpp) outliers start: 33 outliers final: 25 residues processed: 201 average time/residue: 0.1186 time to fit residues: 44.3153 Evaluate side-chains 205 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 912 LEU 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 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 960 LEU 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 825 LEU Chi-restraints excluded: chain D residue 912 LEU Chi-restraints excluded: chain D residue 960 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 254 optimal weight: 10.0000 chunk 221 optimal weight: 30.0000 chunk 296 optimal weight: 3.9990 chunk 427 optimal weight: 5.9990 chunk 236 optimal weight: 30.0000 chunk 78 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 309 optimal weight: 1.9990 chunk 424 optimal weight: 3.9990 chunk 363 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 C 80 HIS D 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.061650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.044227 restraints weight = 151060.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.044487 restraints weight = 70942.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.044608 restraints weight = 40862.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.044858 restraints weight = 35712.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.044930 restraints weight = 34116.257| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4824 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= 0.160 Angle : 0.486 12.275 37140 Z= 0.255 Chirality : 0.039 0.207 4628 Planarity : 0.003 0.036 4908 Dihedral : 4.281 51.037 5216 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.23 % Allowed : 11.08 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.14), residues: 4272 helix: 3.02 (0.10), residues: 2876 sheet: -0.32 (0.28), residues: 268 loop : 0.84 (0.21), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 617 TYR 0.018 0.001 TYR D 952 PHE 0.014 0.001 PHE D 843 TRP 0.015 0.001 TRP C1052 HIS 0.004 0.001 HIS C 903 Details of bonding type rmsd covalent geometry : bond 0.00340 (26744) covalent geometry : angle 0.48628 (37132) SS BOND : bond 0.00067 ( 4) SS BOND : angle 0.31339 ( 8) hydrogen bonds : bond 0.03442 ( 2072) hydrogen bonds : angle 3.55004 ( 6096) ********************** 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 212 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.939 Fit side-chains REVERT: A 81 MET cc_start: 0.6834 (pmm) cc_final: 0.6412 (pmm) REVERT: A 687 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8926 (tpp) REVERT: B 456 MET cc_start: 0.9013 (tpp) cc_final: 0.8810 (tpt) REVERT: B 687 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8926 (tpp) REVERT: C 456 MET cc_start: 0.9006 (tpp) cc_final: 0.8794 (tpt) REVERT: C 687 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8915 (tpp) REVERT: D 81 MET cc_start: 0.6826 (pmm) cc_final: 0.6402 (pmm) REVERT: D 456 MET cc_start: 0.9004 (tpp) cc_final: 0.8793 (tpt) REVERT: D 687 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8923 (tpp) outliers start: 26 outliers final: 21 residues processed: 204 average time/residue: 0.1123 time to fit residues: 42.7255 Evaluate side-chains 211 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 912 LEU 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 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 912 LEU Chi-restraints excluded: chain C residue 960 LEU 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 825 LEU Chi-restraints excluded: chain D residue 912 LEU Chi-restraints excluded: chain D residue 960 LEU 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 340 optimal weight: 0.2980 chunk 391 optimal weight: 4.9990 chunk 252 optimal weight: 8.9990 chunk 216 optimal weight: 50.0000 chunk 416 optimal weight: 4.9990 chunk 352 optimal weight: 40.0000 chunk 404 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 219 optimal weight: 10.0000 chunk 158 optimal weight: 0.0970 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.060627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.042249 restraints weight = 152840.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.043263 restraints weight = 66822.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.043920 restraints weight = 38459.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.044333 restraints weight = 26960.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.044545 restraints weight = 21424.774| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26748 Z= 0.083 Angle : 0.435 12.343 37140 Z= 0.224 Chirality : 0.037 0.212 4628 Planarity : 0.003 0.039 4908 Dihedral : 4.077 54.949 5216 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.95 % Allowed : 12.37 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.57 (0.14), residues: 4272 helix: 3.15 (0.10), residues: 2872 sheet: -0.19 (0.28), residues: 268 loop : 0.97 (0.21), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 617 TYR 0.017 0.001 TYR D1057 PHE 0.013 0.001 PHE C 879 TRP 0.016 0.001 TRP A1052 HIS 0.004 0.001 HIS C 903 Details of bonding type rmsd covalent geometry : bond 0.00172 (26744) covalent geometry : angle 0.43474 (37132) SS BOND : bond 0.00005 ( 4) SS BOND : angle 0.21847 ( 8) hydrogen bonds : bond 0.02762 ( 2072) hydrogen bonds : angle 3.21855 ( 6096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3504.73 seconds wall clock time: 60 minutes 48.73 seconds (3648.73 seconds total)