Starting phenix.real_space_refine on Mon Aug 25 08:00:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srj_40733/08_2025/8srj_40733.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srj_40733/08_2025/8srj_40733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8srj_40733/08_2025/8srj_40733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srj_40733/08_2025/8srj_40733.map" model { file = "/net/cci-nas-00/data/ceres_data/8srj_40733/08_2025/8srj_40733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srj_40733/08_2025/8srj_40733.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26156 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 6455 Classifications: {'peptide': 1074} Incomplete info: {'truncation_to_alanine': 636} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1034} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2184 Unresolved non-hydrogen angles: 2729 Unresolved non-hydrogen dihedrals: 1758 Unresolved non-hydrogen chiralities: 189 Planarities with less than four sites: {'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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, D Time building chain proxies: 8.77, per 1000 atoms: 0.34 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: 2.51 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.96 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: 5.52 Time building geometry restraints manager: 3.20 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 28.220 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.350 ------------------------------------------------------------------------------- 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 aren 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 : 0.970 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: 0.1263 time to fit residues: 67.8590 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 : 0.976 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.064710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.048008 restraints weight = 148539.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.048074 restraints weight = 66129.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.048412 restraints weight = 43721.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.048620 restraints weight = 34529.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.048626 restraints weight = 30228.464| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 aren 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 : 0.906 Fit side-chains REVERT: A 455 MET cc_start: 0.9296 (mpp) cc_final: 0.9004 (mpp) REVERT: A 875 MET cc_start: 0.9398 (ttp) cc_final: 0.8972 (ttm) REVERT: A 981 GLN cc_start: 0.9504 (mt0) cc_final: 0.9247 (mt0) REVERT: B 455 MET cc_start: 0.9293 (mpp) cc_final: 0.8993 (mpp) REVERT: B 981 GLN cc_start: 0.9481 (mt0) cc_final: 0.9212 (mt0) REVERT: C 455 MET cc_start: 0.9305 (mpp) cc_final: 0.9015 (mpp) REVERT: C 875 MET cc_start: 0.9397 (ttp) cc_final: 0.8976 (ttm) REVERT: C 981 GLN cc_start: 0.9484 (mt0) cc_final: 0.9215 (mt0) REVERT: D 455 MET cc_start: 0.9298 (mpp) cc_final: 0.9008 (mpp) REVERT: D 981 GLN cc_start: 0.9479 (mt0) cc_final: 0.9215 (mt0) outliers start: 18 outliers final: 18 residues processed: 207 average time/residue: 0.1100 time to fit residues: 42.0774 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 : 0.981 ------------------------------------------------------------------------------- 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: 0.0980 chunk 333 optimal weight: 0.0870 chunk 48 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 402 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 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: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.065795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047933 restraints weight = 148458.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.049032 restraints weight = 66626.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049730 restraints weight = 38884.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.050043 restraints weight = 27093.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.050389 restraints weight = 22635.329| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2205 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= 0.083 Angle : 0.434 6.211 37140 Z= 0.226 Chirality : 0.036 0.125 4628 Planarity : 0.004 0.038 4908 Dihedral : 4.535 49.001 5216 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.63 % Allowed : 10.82 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.12), residues: 4272 helix: 1.14 (0.09), residues: 2840 sheet: -1.07 (0.27), residues: 272 loop : 0.03 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 617 TYR 0.013 0.001 TYR C1057 PHE 0.013 0.001 PHE A 843 TRP 0.014 0.001 TRP C1052 HIS 0.003 0.000 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00164 (26744) covalent geometry : angle 0.43360 (37132) SS BOND : bond 0.00012 ( 4) SS BOND : angle 0.24021 ( 8) hydrogen bonds : bond 0.02814 ( 2072) hydrogen bonds : angle 3.74973 ( 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 223 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 875 MET cc_start: 0.9315 (ttp) cc_final: 0.8918 (ttm) REVERT: C 875 MET cc_start: 0.9272 (ttp) cc_final: 0.8859 (ttm) REVERT: D 875 MET cc_start: 0.9390 (ttp) cc_final: 0.8971 (ttm) outliers start: 19 outliers final: 11 residues processed: 214 average time/residue: 0.1101 time to fit residues: 43.6000 Evaluate side-chains 203 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 B residue 825 LEU Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 960 LEU 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: 9.9990 chunk 70 optimal weight: 7.9990 chunk 133 optimal weight: 40.0000 chunk 216 optimal weight: 50.0000 chunk 116 optimal weight: 50.0000 chunk 137 optimal weight: 40.0000 chunk 237 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.060097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.042114 restraints weight = 152901.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.042681 restraints weight = 73298.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.043235 restraints weight = 40767.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.043314 restraints weight = 31632.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.043349 restraints weight = 29191.843| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 26748 Z= 0.299 Angle : 0.631 6.338 37140 Z= 0.347 Chirality : 0.042 0.136 4628 Planarity : 0.004 0.043 4908 Dihedral : 5.146 55.266 5216 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.84 % Allowed : 11.77 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.13), residues: 4272 helix: 2.01 (0.10), residues: 2872 sheet: -0.91 (0.27), residues: 260 loop : 0.08 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 913 TYR 0.020 0.002 TYR D1057 PHE 0.015 0.002 PHE B 879 TRP 0.017 0.002 TRP D 726 HIS 0.007 0.002 HIS D 618 Details of bonding type rmsd covalent geometry : bond 0.00632 (26744) covalent geometry : angle 0.63081 (37132) SS BOND : bond 0.00161 ( 4) SS BOND : angle 0.89605 ( 8) hydrogen bonds : bond 0.04415 ( 2072) hydrogen bonds : angle 4.25866 ( 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 217 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.788 Fit side-chains REVERT: A 687 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.9005 (tpp) REVERT: B 687 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.8993 (tpp) REVERT: C 687 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.8990 (tpp) REVERT: D 687 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.8985 (tpp) REVERT: D 875 MET cc_start: 0.9428 (ttp) cc_final: 0.9079 (ttm) outliers start: 33 outliers final: 19 residues processed: 204 average time/residue: 0.1107 time to fit residues: 42.0128 Evaluate side-chains 195 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 991 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 B residue 912 LEU Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 1055 GLN Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 912 LEU 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 817 CYS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 912 LEU Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1055 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 405 optimal weight: 1.9990 chunk 109 optimal weight: 50.0000 chunk 164 optimal weight: 5.9990 chunk 290 optimal weight: 8.9990 chunk 328 optimal weight: 30.0000 chunk 391 optimal weight: 0.6980 chunk 313 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.062674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045451 restraints weight = 151871.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.045652 restraints weight = 75104.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.045840 restraints weight = 41264.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.045928 restraints weight = 37386.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.045990 restraints weight = 33563.059| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26748 Z= 0.135 Angle : 0.450 8.318 37140 Z= 0.241 Chirality : 0.038 0.174 4628 Planarity : 0.003 0.042 4908 Dihedral : 4.462 46.409 5216 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.15 % Allowed : 12.20 % 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 aren not related in a simple way. whole: 2.76 (0.13), residues: 4272 helix: 2.61 (0.10), residues: 2844 sheet: -0.82 (0.28), residues: 260 loop : 0.57 (0.20), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 617 TYR 0.016 0.001 TYR B1057 PHE 0.014 0.001 PHE D 843 TRP 0.017 0.001 TRP B1052 HIS 0.002 0.001 HIS D 715 Details of bonding type rmsd covalent geometry : bond 0.00285 (26744) covalent geometry : angle 0.45042 (37132) SS BOND : bond 0.00126 ( 4) SS BOND : angle 0.20110 ( 8) hydrogen bonds : bond 0.03363 ( 2072) hydrogen bonds : angle 3.62383 ( 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: 25 poor density : 192 time to evaluate : 0.997 Fit side-chains REVERT: A 560 MET cc_start: 0.9231 (mmm) cc_final: 0.9003 (mmm) REVERT: A 687 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8919 (tpp) REVERT: B 560 MET cc_start: 0.9226 (mmm) cc_final: 0.8998 (mmm) REVERT: B 687 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8944 (tpp) REVERT: C 560 MET cc_start: 0.9245 (mmm) cc_final: 0.9000 (mmm) REVERT: C 687 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8927 (tpp) REVERT: D 560 MET cc_start: 0.9221 (mmm) cc_final: 0.8997 (mmm) REVERT: D 687 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8934 (tpp) REVERT: D 875 MET cc_start: 0.9376 (ttp) cc_final: 0.9001 (ttm) outliers start: 25 outliers final: 12 residues processed: 209 average time/residue: 0.1168 time to fit residues: 45.4112 Evaluate side-chains 197 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 B residue 687 MET Chi-restraints excluded: chain B residue 817 CYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 410 optimal weight: 0.9990 chunk 231 optimal weight: 0.7980 chunk 366 optimal weight: 9.9990 chunk 310 optimal weight: 8.9990 chunk 405 optimal weight: 4.9990 chunk 395 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.062929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.045169 restraints weight = 152576.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.045915 restraints weight = 70808.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.046621 restraints weight = 38524.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.046492 restraints weight = 30541.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.046673 restraints weight = 30862.391| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26748 Z= 0.106 Angle : 0.425 8.110 37140 Z= 0.225 Chirality : 0.038 0.201 4628 Planarity : 0.003 0.039 4908 Dihedral : 4.278 50.314 5216 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.84 % Allowed : 11.94 % Favored : 85.22 % 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 aren not related in a simple way. whole: 3.11 (0.14), residues: 4272 helix: 2.84 (0.10), residues: 2876 sheet: -0.76 (0.28), residues: 264 loop : 0.78 (0.21), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 617 TYR 0.016 0.001 TYR A1057 PHE 0.012 0.001 PHE B 843 TRP 0.012 0.001 TRP A1052 HIS 0.002 0.001 HIS C 903 Details of bonding type rmsd covalent geometry : bond 0.00227 (26744) covalent geometry : angle 0.42504 (37132) SS BOND : bond 0.00078 ( 4) SS BOND : angle 0.14990 ( 8) hydrogen bonds : bond 0.02983 ( 2072) hydrogen bonds : angle 3.39361 ( 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: 33 poor density : 193 time to evaluate : 0.722 Fit side-chains REVERT: A 560 MET cc_start: 0.9223 (mmm) cc_final: 0.8968 (mmm) REVERT: A 687 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8849 (tpp) REVERT: B 687 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8836 (tpp) REVERT: C 687 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8838 (tpp) REVERT: D 687 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8844 (tpp) outliers start: 33 outliers final: 15 residues processed: 214 average time/residue: 0.1130 time to fit residues: 44.8965 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 : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 960 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 960 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 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 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: 5.9990 chunk 209 optimal weight: 7.9990 chunk 244 optimal weight: 50.0000 chunk 167 optimal weight: 4.9990 chunk 284 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 352 optimal weight: 50.0000 chunk 80 optimal weight: 7.9990 chunk 405 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.060596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.043538 restraints weight = 155083.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.043220 restraints weight = 78130.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.043463 restraints weight = 54249.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.043568 restraints weight = 41429.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.043674 restraints weight = 37471.324| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 26748 Z= 0.307 Angle : 0.616 7.170 37140 Z= 0.334 Chirality : 0.042 0.142 4628 Planarity : 0.004 0.041 4908 Dihedral : 4.802 42.485 5216 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.18 % Allowed : 11.25 % Favored : 85.57 % 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 aren not related in a simple way. whole: 2.79 (0.13), residues: 4272 helix: 2.61 (0.10), residues: 2876 sheet: -0.62 (0.27), residues: 268 loop : 0.55 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 913 TYR 0.025 0.002 TYR D 952 PHE 0.015 0.002 PHE D1120 TRP 0.013 0.002 TRP C1124 HIS 0.006 0.002 HIS C 682 Details of bonding type rmsd covalent geometry : bond 0.00642 (26744) covalent geometry : angle 0.61557 (37132) SS BOND : bond 0.00152 ( 4) SS BOND : angle 0.92141 ( 8) hydrogen bonds : bond 0.04171 ( 2072) hydrogen bonds : angle 4.11348 ( 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: 37 poor density : 176 time to evaluate : 0.851 Fit side-chains REVERT: A 687 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.8981 (tpp) REVERT: B 687 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.8989 (tpp) REVERT: C 687 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.8985 (tpp) REVERT: D 687 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.8986 (tpp) outliers start: 37 outliers final: 25 residues processed: 205 average time/residue: 0.1067 time to fit residues: 40.2441 Evaluate side-chains 201 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 30.0000 chunk 340 optimal weight: 0.0070 chunk 394 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 chunk 385 optimal weight: 0.6980 chunk 398 optimal weight: 5.9990 chunk 127 optimal weight: 50.0000 chunk 39 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 overall best weight: 2.1002 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.061990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.043788 restraints weight = 153233.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.044741 restraints weight = 69255.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.045167 restraints weight = 41208.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.045667 restraints weight = 31921.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.045881 restraints weight = 25260.652| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26748 Z= 0.116 Angle : 0.453 9.149 37140 Z= 0.240 Chirality : 0.038 0.232 4628 Planarity : 0.003 0.039 4908 Dihedral : 4.423 47.757 5216 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.06 % Allowed : 12.29 % 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 aren not related in a simple way. whole: 3.16 (0.14), residues: 4272 helix: 2.85 (0.10), residues: 2876 sheet: -0.62 (0.28), residues: 260 loop : 0.84 (0.21), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 617 TYR 0.015 0.001 TYR C1057 PHE 0.015 0.001 PHE B 843 TRP 0.016 0.001 TRP C1052 HIS 0.002 0.001 HIS D 903 Details of bonding type rmsd covalent geometry : bond 0.00246 (26744) covalent geometry : angle 0.45354 (37132) SS BOND : bond 0.00093 ( 4) SS BOND : angle 0.09937 ( 8) hydrogen bonds : bond 0.03376 ( 2072) hydrogen bonds : angle 3.48924 ( 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 211 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.853 Fit side-chains REVERT: A 687 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8883 (tpp) REVERT: B 687 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8896 (tpp) REVERT: C 687 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8881 (tpp) REVERT: D 687 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8892 (tpp) outliers start: 24 outliers final: 18 residues processed: 202 average time/residue: 0.1076 time to fit residues: 40.1131 Evaluate side-chains 206 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 960 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 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 960 LEU Chi-restraints excluded: chain D residue 991 LEU 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: 9.9990 chunk 69 optimal weight: 50.0000 chunk 100 optimal weight: 9.9990 chunk 323 optimal weight: 40.0000 chunk 18 optimal weight: 0.0270 chunk 113 optimal weight: 50.0000 chunk 319 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 216 optimal weight: 50.0000 chunk 63 optimal weight: 0.0670 chunk 408 optimal weight: 7.9990 overall best weight: 2.2180 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.062129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.044028 restraints weight = 153030.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.044930 restraints weight = 68614.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.045537 restraints weight = 40851.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.045938 restraints weight = 29428.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.046052 restraints weight = 23965.405| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 26748 Z= 0.118 Angle : 0.455 8.433 37140 Z= 0.238 Chirality : 0.038 0.198 4628 Planarity : 0.003 0.038 4908 Dihedral : 4.341 47.678 5216 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.23 % Allowed : 12.63 % Favored : 85.14 % 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 aren not related in a simple way. whole: 3.35 (0.14), residues: 4272 helix: 2.98 (0.10), residues: 2876 sheet: -0.54 (0.28), residues: 272 loop : 0.98 (0.21), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 617 TYR 0.017 0.001 TYR D 952 PHE 0.012 0.001 PHE B 843 TRP 0.013 0.001 TRP A1052 HIS 0.004 0.001 HIS C 903 Details of bonding type rmsd covalent geometry : bond 0.00254 (26744) covalent geometry : angle 0.45481 (37132) SS BOND : bond 0.00087 ( 4) SS BOND : angle 0.19921 ( 8) hydrogen bonds : bond 0.03173 ( 2072) hydrogen bonds : angle 3.41077 ( 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 214 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 1.002 Fit side-chains REVERT: A 687 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8837 (tpp) REVERT: B 81 MET cc_start: 0.6568 (ptp) cc_final: 0.6363 (pmm) REVERT: B 687 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8832 (tpp) REVERT: C 687 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8831 (tpp) REVERT: D 81 MET cc_start: 0.6747 (ptp) cc_final: 0.6414 (pmm) REVERT: D 687 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8825 (tpp) outliers start: 26 outliers final: 20 residues processed: 206 average time/residue: 0.1160 time to fit residues: 44.4770 Evaluate side-chains 212 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 960 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 960 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 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 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 254 optimal weight: 20.0000 chunk 221 optimal weight: 30.0000 chunk 296 optimal weight: 3.9990 chunk 427 optimal weight: 5.9990 chunk 236 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 309 optimal weight: 1.9990 chunk 424 optimal weight: 3.9990 chunk 363 optimal weight: 10.0000 chunk 157 optimal weight: 0.0030 overall best weight: 1.5796 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.062715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.045490 restraints weight = 150353.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.046020 restraints weight = 69592.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.046149 restraints weight = 37457.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.046228 restraints weight = 36797.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.046258 restraints weight = 33512.405| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4565 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= 0.097 Angle : 0.442 8.725 37140 Z= 0.230 Chirality : 0.038 0.197 4628 Planarity : 0.003 0.038 4908 Dihedral : 4.227 47.829 5216 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.89 % Allowed : 13.06 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.48 (0.14), residues: 4272 helix: 3.07 (0.10), residues: 2876 sheet: -0.40 (0.29), residues: 260 loop : 1.00 (0.21), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 617 TYR 0.017 0.001 TYR D 952 PHE 0.011 0.001 PHE D 843 TRP 0.014 0.001 TRP C1052 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00208 (26744) covalent geometry : angle 0.44219 (37132) SS BOND : bond 0.00048 ( 4) SS BOND : angle 0.05843 ( 8) hydrogen bonds : bond 0.02943 ( 2072) hydrogen bonds : angle 3.27923 ( 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 210 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.921 Fit side-chains REVERT: B 81 MET cc_start: 0.6678 (ptp) cc_final: 0.6437 (pmm) REVERT: C 456 MET cc_start: 0.8901 (tpp) cc_final: 0.8695 (tpt) REVERT: D 81 MET cc_start: 0.6683 (ptp) cc_final: 0.6435 (pmm) REVERT: D 456 MET cc_start: 0.8912 (tpp) cc_final: 0.8706 (tpt) outliers start: 22 outliers final: 17 residues processed: 202 average time/residue: 0.1126 time to fit residues: 42.3846 Evaluate side-chains 205 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1121 LEU Chi-restraints excluded: chain D residue 817 CYS 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: 0.9990 chunk 391 optimal weight: 0.6980 chunk 252 optimal weight: 9.9990 chunk 216 optimal weight: 50.0000 chunk 416 optimal weight: 4.9990 chunk 352 optimal weight: 50.0000 chunk 404 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 219 optimal weight: 6.9990 chunk 158 optimal weight: 0.0870 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS C 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.062086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.044077 restraints weight = 152632.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.045060 restraints weight = 68534.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.045695 restraints weight = 40075.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.046100 restraints weight = 28657.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.046289 restraints weight = 23097.452| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26748 Z= 0.080 Angle : 0.429 9.444 37140 Z= 0.220 Chirality : 0.037 0.193 4628 Planarity : 0.003 0.039 4908 Dihedral : 4.037 42.413 5216 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.12 % Allowed : 13.57 % Favored : 85.31 % 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 aren not related in a simple way. whole: 3.61 (0.14), residues: 4272 helix: 3.16 (0.10), residues: 2876 sheet: -0.20 (0.29), residues: 268 loop : 1.03 (0.21), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 617 TYR 0.014 0.001 TYR A1057 PHE 0.011 0.001 PHE B 879 TRP 0.013 0.001 TRP C1052 HIS 0.005 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00166 (26744) covalent geometry : angle 0.42856 (37132) SS BOND : bond 0.00041 ( 4) SS BOND : angle 0.16097 ( 8) hydrogen bonds : bond 0.02637 ( 2072) hydrogen bonds : angle 3.14630 ( 6096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3359.74 seconds wall clock time: 58 minutes 24.08 seconds (3504.08 seconds total)