Starting phenix.real_space_refine on Tue Jun 24 08:01:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w9e_32365/06_2025/7w9e_32365.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9e_32365/06_2025/7w9e_32365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w9e_32365/06_2025/7w9e_32365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9e_32365/06_2025/7w9e_32365.map" model { file = "/net/cci-nas-00/data/ceres_data/7w9e_32365/06_2025/7w9e_32365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9e_32365/06_2025/7w9e_32365.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.075 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 128 5.16 5 C 17935 2.51 5 N 4723 2.21 5 O 5395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 204 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28181 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "B" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "C" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "D" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1671 Classifications: {'peptide': 220} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 202} Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1643 Classifications: {'peptide': 211} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 7, 'TRANS': 200} Time building chain proxies: 15.96, per 1000 atoms: 0.57 Number of scatterers: 28181 At special positions: 0 Unit cell: (157.392, 144.276, 260.134, 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 128 16.00 O 5395 8.00 N 4723 7.00 C 17935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " 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: 6.99 Conformation dependent library (CDL) restraints added in 3.8 seconds 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6748 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 63 sheets defined 21.1% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.90 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.114A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 389' Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.658A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.817A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.553A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.819A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.551A pdb=" N ALA A 924 " --> pdb=" O GLN A 920 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.847A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.800A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.500A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.758A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.208A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.208A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.514A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.560A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.551A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.612A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.733A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.234A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.129A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.536A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.544A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.976A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.548A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.507A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.651A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.706A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.555A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.918A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.602A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.508A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.974A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.122A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.457A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1140 through 1145' Processing helix chain 'D' and resid 62 through 65 removed outlier: 4.070A pdb=" N LYS D 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 90 removed outlier: 3.627A pdb=" N ASP D 90 " --> pdb=" O THR D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.627A pdb=" N TYR D 104 " --> pdb=" O TYR D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.796A pdb=" N LEU E 83 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 182 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.548A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.518A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 67 removed outlier: 4.245A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 63 through 67 removed outlier: 4.245A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.566A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 317 removed outlier: 7.407A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.533A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.826A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.826A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.996A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.093A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.576A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.247A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.791A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'B' and resid 28 through 30 removed outlier: 4.573A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.919A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.996A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.537A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.798A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 327 through 328 removed outlier: 3.615A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.520A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.512A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.530A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.148A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 712 through 713 removed outlier: 3.599A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 721 Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 721 removed outlier: 3.605A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.297A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.783A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.297A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.568A pdb=" N TYR C 279 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.025A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.501A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.634A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.554A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.124A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.673A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.367A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF9, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.758A pdb=" N VAL D 18 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS D 22 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.558A pdb=" N GLU D 10 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 117 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LYS D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TRP D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER D 40 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU D 45 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY D 50 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 59 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 129 through 130 removed outlier: 3.658A pdb=" N VAL D 143 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 188 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS D 147 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 186 " --> pdb=" O CYS D 147 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 184 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR D 182 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 129 through 130 removed outlier: 3.658A pdb=" N VAL D 143 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 188 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS D 147 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 186 " --> pdb=" O CYS D 147 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 184 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR D 182 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.664A pdb=" N THR D 211 " --> pdb=" O HIS D 206 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.675A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR E 72 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AG7, first strand: chain 'E' and resid 45 through 49 removed outlier: 6.729A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR E 49 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.841A pdb=" N ASN E 137 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 153 through 154 removed outlier: 3.792A pdb=" N ASN E 145 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS E 149 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR E 193 " --> pdb=" O LYS E 149 " (cutoff:3.500A) 1003 hydrogen bonds defined for protein. 2718 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: 14.37 Time building geometry restraints manager: 8.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9107 1.34 - 1.46: 7138 1.46 - 1.59: 12425 1.59 - 1.71: 0 1.71 - 1.83: 164 Bond restraints: 28834 Sorted by residual: bond pdb=" N GLN C 14 " pdb=" CA GLN C 14 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.29e+00 bond pdb=" N GLN A 14 " pdb=" CA GLN A 14 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" N GLN B 14 " pdb=" CA GLN B 14 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" CA PRO D 133 " pdb=" C PRO D 133 " ideal model delta sigma weight residual 1.516 1.539 -0.022 1.42e-02 4.96e+03 2.49e+00 bond pdb=" N THR E 51 " pdb=" CA THR E 51 " ideal model delta sigma weight residual 1.462 1.484 -0.022 1.48e-02 4.57e+03 2.29e+00 ... (remaining 28829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 38834 2.14 - 4.27: 307 4.27 - 6.41: 76 6.41 - 8.54: 5 8.54 - 10.68: 1 Bond angle restraints: 39223 Sorted by residual: angle pdb=" C PRO D 133 " pdb=" N GLY D 134 " pdb=" CA GLY D 134 " ideal model delta sigma weight residual 121.70 132.38 -10.68 1.80e+00 3.09e-01 3.52e+01 angle pdb=" C SER E 50 " pdb=" N THR E 51 " pdb=" CA THR E 51 " ideal model delta sigma weight residual 122.61 129.73 -7.12 1.56e+00 4.11e-01 2.08e+01 angle pdb=" CA PRO D 133 " pdb=" C PRO D 133 " pdb=" N GLY D 134 " ideal model delta sigma weight residual 117.98 123.80 -5.82 1.43e+00 4.89e-01 1.65e+01 angle pdb=" N PRO D 133 " pdb=" CA PRO D 133 " pdb=" C PRO D 133 " ideal model delta sigma weight residual 113.40 118.54 -5.14 1.34e+00 5.57e-01 1.47e+01 angle pdb=" N LYS C 97 " pdb=" CA LYS C 97 " pdb=" C LYS C 97 " ideal model delta sigma weight residual 113.43 109.36 4.07 1.26e+00 6.30e-01 1.04e+01 ... (remaining 39218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 15882 17.87 - 35.74: 1096 35.74 - 53.61: 160 53.61 - 71.48: 35 71.48 - 89.35: 29 Dihedral angle restraints: 17202 sinusoidal: 6702 harmonic: 10500 Sorted by residual: dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " pdb=" CB CYS E 88 " ideal model delta sinusoidal sigma weight residual 93.00 140.40 -47.40 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CA TYR D 105 " pdb=" C TYR D 105 " pdb=" N ALA D 106 " pdb=" CA ALA D 106 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" SG CYS C 738 " pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " pdb=" CA CYS C 760 " ideal model delta sinusoidal sigma weight residual -73.00 -5.18 -67.82 1 2.00e+01 2.50e-03 1.49e+01 ... (remaining 17199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3538 0.047 - 0.094: 591 0.094 - 0.141: 284 0.141 - 0.188: 8 0.188 - 0.236: 3 Chirality restraints: 4424 Sorted by residual: chirality pdb=" CA PRO D 133 " pdb=" N PRO D 133 " pdb=" C PRO D 133 " pdb=" CB PRO D 133 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA THR E 51 " pdb=" N THR E 51 " pdb=" C THR E 51 " pdb=" CB THR E 51 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 4421 not shown) Planarity restraints: 5084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 101 " -0.032 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO D 102 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 102 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 102 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 155 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO D 156 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 132 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.53e+00 pdb=" N PRO D 133 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 133 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 133 " -0.026 5.00e-02 4.00e+02 ... (remaining 5081 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 266 2.60 - 3.18: 23314 3.18 - 3.75: 41062 3.75 - 4.33: 58897 4.33 - 4.90: 98243 Nonbonded interactions: 221782 Sorted by model distance: nonbonded pdb=" CE LYS C 478 " pdb=" CE1 TYR E 96 " model vdw 2.028 3.740 nonbonded pdb=" OE1 GLN A 965 " pdb=" OG SER A1003 " model vdw 2.078 3.040 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.080 3.040 nonbonded pdb=" OG SER A 968 " pdb=" O GLN B 755 " model vdw 2.100 3.040 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.105 3.040 ... (remaining 221777 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' selection = chain 'B' selection = chain 'C' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.240 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 67.850 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 : 0.004 0.044 28877 Z= 0.166 Angle : 0.584 10.678 39309 Z= 0.311 Chirality : 0.044 0.236 4424 Planarity : 0.004 0.048 5084 Dihedral : 12.891 89.351 10325 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.11), residues: 3565 helix: -2.78 (0.13), residues: 659 sheet: -2.51 (0.15), residues: 851 loop : -2.65 (0.11), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 195 HIS 0.004 0.001 HIS A1083 PHE 0.012 0.001 PHE E 139 TYR 0.011 0.001 TYR C 144 ARG 0.005 0.000 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.28173 ( 971) hydrogen bonds : angle 9.82996 ( 2718) SS BOND : bond 0.00215 ( 43) SS BOND : angle 0.85047 ( 86) covalent geometry : bond 0.00380 (28834) covalent geometry : angle 0.58367 (39223) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 555 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 790 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7777 (mmmm) REVERT: B 521 PRO cc_start: 0.6758 (Cg_exo) cc_final: 0.6525 (Cg_endo) REVERT: B 735 SER cc_start: 0.8408 (t) cc_final: 0.8127 (p) REVERT: C 105 ILE cc_start: 0.8179 (mt) cc_final: 0.7935 (pt) REVERT: C 200 TYR cc_start: 0.5499 (m-80) cc_final: 0.5220 (m-10) REVERT: C 212 LEU cc_start: 0.6130 (tp) cc_final: 0.5855 (mt) REVERT: C 338 PHE cc_start: 0.6867 (m-80) cc_final: 0.6642 (m-80) REVERT: C 342 PHE cc_start: 0.7601 (m-80) cc_final: 0.6559 (m-80) REVERT: C 1005 GLN cc_start: 0.7521 (mt0) cc_final: 0.7215 (mt0) outliers start: 0 outliers final: 0 residues processed: 555 average time/residue: 0.4170 time to fit residues: 357.5901 Evaluate side-chains 271 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 327 optimal weight: 0.6980 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 950 ASN A 978 ASN B 115 GLN B 354 ASN B 414 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1002 GLN C 66 HIS C 487 ASN C 655 HIS C 955 ASN C1010 GLN C1071 GLN D 5 GLN D 112 GLN D 140 ASN E 8 GLN E 145 ASN E 161 ASN E 166 GLN E 190 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.125121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.096968 restraints weight = 89136.004| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.20 r_work: 0.3508 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28877 Z= 0.161 Angle : 0.580 9.747 39309 Z= 0.306 Chirality : 0.046 0.181 4424 Planarity : 0.004 0.057 5084 Dihedral : 4.247 17.642 3874 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.30 % Allowed : 8.18 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.13), residues: 3565 helix: -0.22 (0.19), residues: 682 sheet: -1.59 (0.15), residues: 894 loop : -2.03 (0.12), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 258 HIS 0.004 0.001 HIS A 655 PHE 0.021 0.002 PHE C 643 TYR 0.019 0.002 TYR A1067 ARG 0.007 0.001 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.04959 ( 971) hydrogen bonds : angle 6.09672 ( 2718) SS BOND : bond 0.00765 ( 43) SS BOND : angle 1.53531 ( 86) covalent geometry : bond 0.00368 (28834) covalent geometry : angle 0.57609 (39223) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 297 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7680 (tm-30) REVERT: A 703 ASN cc_start: 0.8026 (m110) cc_final: 0.7707 (m110) REVERT: A 858 LEU cc_start: 0.8810 (mp) cc_final: 0.8602 (pt) REVERT: A 964 LYS cc_start: 0.9136 (mtpt) cc_final: 0.8933 (mtpp) REVERT: A 985 ASP cc_start: 0.8185 (m-30) cc_final: 0.7516 (m-30) REVERT: B 394 ASN cc_start: 0.6246 (m-40) cc_final: 0.5968 (m110) REVERT: C 270 LEU cc_start: 0.8318 (mt) cc_final: 0.8020 (mt) REVERT: C 481 ASN cc_start: 0.4604 (m-40) cc_final: 0.4110 (t0) REVERT: C 869 MET cc_start: 0.8899 (mtp) cc_final: 0.8618 (mtp) REVERT: D 34 MET cc_start: 0.2813 (mpp) cc_final: 0.2455 (mpp) outliers start: 41 outliers final: 23 residues processed: 323 average time/residue: 0.3938 time to fit residues: 205.7973 Evaluate side-chains 241 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 88 optimal weight: 4.9990 chunk 345 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 196 ASN A 901 GLN A 935 GLN A1010 GLN B 99 ASN B 134 GLN B 314 GLN B 354 ASN B 498 GLN B 501 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN C 66 HIS E 37 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.121499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.092322 restraints weight = 90127.005| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.48 r_work: 0.3428 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28877 Z= 0.229 Angle : 0.615 9.363 39309 Z= 0.324 Chirality : 0.047 0.188 4424 Planarity : 0.004 0.080 5084 Dihedral : 4.597 19.220 3874 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.12 % Allowed : 10.34 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.13), residues: 3565 helix: 0.49 (0.20), residues: 674 sheet: -1.18 (0.16), residues: 936 loop : -1.86 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 886 HIS 0.019 0.001 HIS C 66 PHE 0.019 0.002 PHE B 515 TYR 0.036 0.002 TYR C 707 ARG 0.010 0.001 ARG B 357 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 971) hydrogen bonds : angle 5.84622 ( 2718) SS BOND : bond 0.00390 ( 43) SS BOND : angle 1.31859 ( 86) covalent geometry : bond 0.00528 (28834) covalent geometry : angle 0.61291 (39223) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 225 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8581 (mt) cc_final: 0.8321 (tt) REVERT: A 129 LYS cc_start: 0.8071 (mttt) cc_final: 0.7825 (ttmt) REVERT: A 207 HIS cc_start: 0.6126 (OUTLIER) cc_final: 0.5830 (t-90) REVERT: A 468 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7318 (mm) REVERT: A 613 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8120 (mp10) REVERT: A 661 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 985 ASP cc_start: 0.8444 (m-30) cc_final: 0.8184 (m-30) REVERT: B 191 GLU cc_start: 0.5832 (tt0) cc_final: 0.5617 (tt0) REVERT: B 357 ARG cc_start: 0.7910 (mtp-110) cc_final: 0.6919 (mtp180) REVERT: B 394 ASN cc_start: 0.6762 (m-40) cc_final: 0.5938 (m110) REVERT: C 66 HIS cc_start: 0.4665 (t70) cc_final: 0.4417 (t-90) REVERT: C 177 MET cc_start: 0.2905 (ttt) cc_final: 0.2494 (ttt) REVERT: D 3 GLN cc_start: 0.4692 (pm20) cc_final: 0.4216 (pp30) outliers start: 67 outliers final: 42 residues processed: 275 average time/residue: 0.3744 time to fit residues: 168.2569 Evaluate side-chains 222 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 165 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 7.9990 chunk 345 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 293 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 224 optimal weight: 0.0170 chunk 257 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 914 ASN B 955 ASN B 965 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.122400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.093716 restraints weight = 89810.939| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.38 r_work: 0.3446 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28877 Z= 0.127 Angle : 0.519 8.633 39309 Z= 0.271 Chirality : 0.044 0.156 4424 Planarity : 0.004 0.073 5084 Dihedral : 4.265 20.261 3874 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.87 % Allowed : 12.08 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.14), residues: 3565 helix: 1.03 (0.21), residues: 665 sheet: -0.85 (0.17), residues: 920 loop : -1.61 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 258 HIS 0.004 0.001 HIS A 49 PHE 0.022 0.001 PHE A 32 TYR 0.031 0.001 TYR C 707 ARG 0.010 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 971) hydrogen bonds : angle 5.40081 ( 2718) SS BOND : bond 0.00281 ( 43) SS BOND : angle 1.09536 ( 86) covalent geometry : bond 0.00293 (28834) covalent geometry : angle 0.51746 (39223) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 217 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8010 (mttt) cc_final: 0.7791 (tttt) REVERT: A 468 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7277 (mm) REVERT: A 613 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8157 (mp10) REVERT: A 661 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7654 (tm-30) REVERT: A 985 ASP cc_start: 0.8458 (m-30) cc_final: 0.8209 (m-30) REVERT: B 394 ASN cc_start: 0.6686 (m-40) cc_final: 0.6453 (m110) REVERT: B 933 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8704 (mtpp) REVERT: C 41 LYS cc_start: 0.7774 (mttt) cc_final: 0.7510 (mmmt) REVERT: C 53 ASP cc_start: 0.7866 (m-30) cc_final: 0.7521 (m-30) REVERT: C 94 SER cc_start: 0.7246 (m) cc_final: 0.6862 (p) REVERT: C 177 MET cc_start: 0.2669 (ttt) cc_final: 0.2217 (ttt) REVERT: C 270 LEU cc_start: 0.8388 (mt) cc_final: 0.8166 (mt) REVERT: C 519 HIS cc_start: 0.5811 (OUTLIER) cc_final: 0.5362 (p90) REVERT: C 651 ILE cc_start: 0.9336 (pt) cc_final: 0.9098 (mp) REVERT: C 869 MET cc_start: 0.8931 (mtp) cc_final: 0.8718 (mtp) REVERT: D 3 GLN cc_start: 0.4679 (pm20) cc_final: 0.4272 (pp30) REVERT: D 81 MET cc_start: -0.0391 (tpp) cc_final: -0.0918 (mmm) outliers start: 59 outliers final: 33 residues processed: 260 average time/residue: 0.3723 time to fit residues: 158.9279 Evaluate side-chains 214 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 174 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 chunk 255 optimal weight: 0.0270 chunk 126 optimal weight: 7.9990 chunk 176 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 213 optimal weight: 0.0370 chunk 58 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 764 ASN B 69 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 914 ASN C 658 ASN C 935 GLN C 957 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.123139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.094645 restraints weight = 89666.674| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.41 r_work: 0.3470 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28877 Z= 0.094 Angle : 0.486 8.771 39309 Z= 0.252 Chirality : 0.043 0.171 4424 Planarity : 0.004 0.061 5084 Dihedral : 3.975 19.521 3874 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.52 % Allowed : 12.75 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3565 helix: 1.33 (0.21), residues: 672 sheet: -0.62 (0.17), residues: 908 loop : -1.41 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 258 HIS 0.003 0.001 HIS C 66 PHE 0.019 0.001 PHE A 32 TYR 0.027 0.001 TYR C 707 ARG 0.007 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 971) hydrogen bonds : angle 5.10555 ( 2718) SS BOND : bond 0.00221 ( 43) SS BOND : angle 0.92344 ( 86) covalent geometry : bond 0.00206 (28834) covalent geometry : angle 0.48428 (39223) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8037 (mttt) cc_final: 0.7814 (ttmt) REVERT: A 468 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7365 (mm) REVERT: A 613 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8231 (mp10) REVERT: A 661 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 985 ASP cc_start: 0.8559 (m-30) cc_final: 0.7777 (m-30) REVERT: B 933 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8714 (mtpp) REVERT: C 41 LYS cc_start: 0.7801 (mttt) cc_final: 0.7513 (mmmt) REVERT: C 53 ASP cc_start: 0.7747 (m-30) cc_final: 0.7455 (m-30) REVERT: C 94 SER cc_start: 0.7419 (m) cc_final: 0.7030 (p) REVERT: C 177 MET cc_start: 0.2771 (ttt) cc_final: 0.2063 (ttt) REVERT: C 269 TYR cc_start: 0.7938 (m-80) cc_final: 0.7697 (m-80) REVERT: C 519 HIS cc_start: 0.5763 (OUTLIER) cc_final: 0.5343 (p90) REVERT: D 3 GLN cc_start: 0.4757 (pm20) cc_final: 0.4201 (pp30) REVERT: D 81 MET cc_start: 0.0013 (tpp) cc_final: -0.0200 (mmm) REVERT: E 24 LYS cc_start: 0.3177 (OUTLIER) cc_final: 0.2580 (mttp) outliers start: 48 outliers final: 31 residues processed: 248 average time/residue: 0.3782 time to fit residues: 154.1993 Evaluate side-chains 226 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 24 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 37 optimal weight: 7.9990 chunk 116 optimal weight: 0.0050 chunk 267 optimal weight: 0.0060 chunk 100 optimal weight: 1.9990 chunk 297 optimal weight: 0.7980 chunk 333 optimal weight: 0.3980 chunk 140 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 179 optimal weight: 0.0060 chunk 136 optimal weight: 0.0370 chunk 266 optimal weight: 1.9990 overall best weight: 0.0904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B 498 GLN B 787 GLN B 901 GLN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.126752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.097902 restraints weight = 90933.561| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.29 r_work: 0.3497 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 28877 Z= 0.086 Angle : 0.473 10.450 39309 Z= 0.243 Chirality : 0.042 0.232 4424 Planarity : 0.003 0.052 5084 Dihedral : 3.712 18.296 3874 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.62 % Allowed : 12.90 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3565 helix: 1.52 (0.21), residues: 669 sheet: -0.46 (0.17), residues: 933 loop : -1.18 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.002 0.000 HIS C 66 PHE 0.016 0.001 PHE A 32 TYR 0.026 0.001 TYR A 707 ARG 0.006 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 971) hydrogen bonds : angle 4.86240 ( 2718) SS BOND : bond 0.00275 ( 43) SS BOND : angle 1.21988 ( 86) covalent geometry : bond 0.00187 (28834) covalent geometry : angle 0.47003 (39223) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 234 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8027 (mttt) cc_final: 0.7701 (ttmt) REVERT: A 468 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7369 (mm) REVERT: A 523 THR cc_start: 0.8019 (p) cc_final: 0.7568 (t) REVERT: A 661 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7619 (tm-30) REVERT: A 745 ASP cc_start: 0.7816 (m-30) cc_final: 0.7561 (m-30) REVERT: A 1019 ARG cc_start: 0.8826 (ttp-110) cc_final: 0.8538 (ttm110) REVERT: B 933 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8692 (mtpp) REVERT: C 94 SER cc_start: 0.7321 (m) cc_final: 0.7004 (p) REVERT: C 128 ILE cc_start: 0.8736 (mp) cc_final: 0.8532 (mp) REVERT: C 177 MET cc_start: 0.2824 (ttt) cc_final: 0.2287 (ttt) REVERT: C 270 LEU cc_start: 0.8367 (mt) cc_final: 0.8157 (mt) REVERT: C 519 HIS cc_start: 0.5693 (OUTLIER) cc_final: 0.5331 (p90) REVERT: C 571 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8188 (t70) REVERT: D 3 GLN cc_start: 0.4802 (pm20) cc_final: 0.4320 (pp30) REVERT: E 24 LYS cc_start: 0.2877 (OUTLIER) cc_final: 0.2161 (mttp) REVERT: E 123 GLU cc_start: 0.2383 (mp0) cc_final: 0.1045 (tp30) REVERT: E 179 LEU cc_start: 0.0683 (tt) cc_final: 0.0305 (tp) outliers start: 51 outliers final: 28 residues processed: 272 average time/residue: 0.3502 time to fit residues: 160.5821 Evaluate side-chains 233 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 353 optimal weight: 0.6980 chunk 301 optimal weight: 0.5980 chunk 312 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 344 optimal weight: 0.1980 chunk 219 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 354 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 914 ASN B 343 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.121432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092651 restraints weight = 89294.460| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.39 r_work: 0.3434 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28877 Z= 0.156 Angle : 0.537 9.900 39309 Z= 0.279 Chirality : 0.044 0.247 4424 Planarity : 0.004 0.054 5084 Dihedral : 4.111 18.138 3874 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.97 % Allowed : 12.84 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3565 helix: 1.48 (0.21), residues: 668 sheet: -0.48 (0.17), residues: 931 loop : -1.26 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 258 HIS 0.003 0.001 HIS A 49 PHE 0.016 0.002 PHE A 32 TYR 0.032 0.001 TYR A 707 ARG 0.005 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 971) hydrogen bonds : angle 5.08218 ( 2718) SS BOND : bond 0.00544 ( 43) SS BOND : angle 1.33020 ( 86) covalent geometry : bond 0.00361 (28834) covalent geometry : angle 0.53427 (39223) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 201 time to evaluate : 4.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8120 (mttt) cc_final: 0.7867 (ttmt) REVERT: A 468 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7295 (mm) REVERT: A 661 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7722 (tm-30) REVERT: B 515 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.5643 (p90) REVERT: B 933 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8697 (mtpp) REVERT: C 41 LYS cc_start: 0.7939 (mttt) cc_final: 0.7630 (mmmt) REVERT: C 94 SER cc_start: 0.7238 (m) cc_final: 0.6950 (p) REVERT: C 177 MET cc_start: 0.2731 (ttt) cc_final: 0.2190 (ttt) REVERT: C 202 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8230 (ttpp) REVERT: C 519 HIS cc_start: 0.5782 (OUTLIER) cc_final: 0.5444 (p90) REVERT: C 900 MET cc_start: 0.9058 (mmm) cc_final: 0.8567 (mtt) REVERT: C 1001 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9088 (mp) REVERT: D 3 GLN cc_start: 0.4691 (pm20) cc_final: 0.4011 (pp30) REVERT: E 24 LYS cc_start: 0.3232 (OUTLIER) cc_final: 0.2501 (mttp) outliers start: 62 outliers final: 44 residues processed: 254 average time/residue: 0.4834 time to fit residues: 211.3612 Evaluate side-chains 235 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 184 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 23 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 317 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 320 optimal weight: 0.0020 chunk 316 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 914 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.122368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.093621 restraints weight = 89960.165| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.41 r_work: 0.3452 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28877 Z= 0.111 Angle : 0.501 10.236 39309 Z= 0.258 Chirality : 0.043 0.248 4424 Planarity : 0.004 0.054 5084 Dihedral : 3.962 19.389 3874 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.55 % Allowed : 13.44 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3565 helix: 1.60 (0.21), residues: 666 sheet: -0.37 (0.17), residues: 941 loop : -1.26 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 258 HIS 0.005 0.001 HIS C 245 PHE 0.022 0.001 PHE A 238 TYR 0.032 0.001 TYR A 707 ARG 0.005 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 971) hydrogen bonds : angle 4.90155 ( 2718) SS BOND : bond 0.00254 ( 43) SS BOND : angle 1.17153 ( 86) covalent geometry : bond 0.00257 (28834) covalent geometry : angle 0.49856 (39223) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8094 (mttt) cc_final: 0.7823 (ttmt) REVERT: A 468 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7254 (mm) REVERT: A 661 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7665 (tm-30) REVERT: A 745 ASP cc_start: 0.7844 (m-30) cc_final: 0.7568 (m-30) REVERT: B 933 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8713 (mtpp) REVERT: C 41 LYS cc_start: 0.7907 (mttt) cc_final: 0.7630 (mmmt) REVERT: C 94 SER cc_start: 0.7352 (m) cc_final: 0.7059 (p) REVERT: C 177 MET cc_start: 0.2553 (ttt) cc_final: 0.2131 (ttt) REVERT: C 900 MET cc_start: 0.9047 (mmm) cc_final: 0.8550 (mtt) REVERT: D 3 GLN cc_start: 0.4361 (pm20) cc_final: 0.3490 (pp30) REVERT: D 34 MET cc_start: 0.1195 (ptp) cc_final: 0.0838 (ptp) REVERT: E 4 MET cc_start: 0.2019 (tmm) cc_final: 0.1682 (ppp) outliers start: 49 outliers final: 38 residues processed: 241 average time/residue: 0.3535 time to fit residues: 143.5583 Evaluate side-chains 226 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 159 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 333 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 234 optimal weight: 0.0000 chunk 76 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 914 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.122164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.094019 restraints weight = 90087.372| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.40 r_work: 0.3446 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 28877 Z= 0.101 Angle : 0.492 10.273 39309 Z= 0.252 Chirality : 0.043 0.244 4424 Planarity : 0.003 0.051 5084 Dihedral : 3.878 18.549 3874 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.36 % Allowed : 13.60 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3565 helix: 1.72 (0.21), residues: 665 sheet: -0.31 (0.17), residues: 953 loop : -1.18 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 258 HIS 0.002 0.000 HIS D 206 PHE 0.019 0.001 PHE A 238 TYR 0.033 0.001 TYR A 707 ARG 0.005 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 971) hydrogen bonds : angle 4.81011 ( 2718) SS BOND : bond 0.00263 ( 43) SS BOND : angle 1.11751 ( 86) covalent geometry : bond 0.00234 (28834) covalent geometry : angle 0.48976 (39223) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8039 (mttt) cc_final: 0.7763 (ttmt) REVERT: A 241 LEU cc_start: 0.8100 (mt) cc_final: 0.7740 (pp) REVERT: A 468 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7258 (mm) REVERT: A 661 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 745 ASP cc_start: 0.7872 (m-30) cc_final: 0.7568 (m-30) REVERT: B 933 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8690 (mtpp) REVERT: C 41 LYS cc_start: 0.7909 (mttt) cc_final: 0.7610 (mmmt) REVERT: C 53 ASP cc_start: 0.7844 (m-30) cc_final: 0.7491 (m-30) REVERT: C 94 SER cc_start: 0.7327 (m) cc_final: 0.7042 (p) REVERT: C 177 MET cc_start: 0.2618 (ttt) cc_final: 0.2203 (ttt) REVERT: C 900 MET cc_start: 0.9064 (mmm) cc_final: 0.8542 (mtt) REVERT: D 3 GLN cc_start: 0.4253 (pm20) cc_final: 0.3554 (pp30) REVERT: E 4 MET cc_start: 0.1925 (tmm) cc_final: 0.1595 (ppp) outliers start: 43 outliers final: 40 residues processed: 233 average time/residue: 0.3827 time to fit residues: 150.7091 Evaluate side-chains 233 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 29 optimal weight: 0.3980 chunk 158 optimal weight: 7.9990 chunk 204 optimal weight: 0.6980 chunk 258 optimal weight: 3.9990 chunk 281 optimal weight: 0.9980 chunk 31 optimal weight: 0.0570 chunk 324 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.122172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.093716 restraints weight = 89633.419| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.46 r_work: 0.3458 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 28877 Z= 0.103 Angle : 0.493 10.291 39309 Z= 0.253 Chirality : 0.043 0.174 4424 Planarity : 0.004 0.052 5084 Dihedral : 3.863 20.445 3874 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.49 % Allowed : 13.57 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3565 helix: 1.80 (0.21), residues: 659 sheet: -0.24 (0.17), residues: 952 loop : -1.14 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 258 HIS 0.002 0.001 HIS D 206 PHE 0.019 0.001 PHE A 238 TYR 0.037 0.001 TYR A 707 ARG 0.005 0.000 ARG C 319 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 971) hydrogen bonds : angle 4.74256 ( 2718) SS BOND : bond 0.00245 ( 43) SS BOND : angle 1.09594 ( 86) covalent geometry : bond 0.00238 (28834) covalent geometry : angle 0.49079 (39223) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.3983 (mttt) cc_final: 0.3534 (tttt) REVERT: A 129 LYS cc_start: 0.7940 (mttt) cc_final: 0.7711 (ttmt) REVERT: A 241 LEU cc_start: 0.8179 (mt) cc_final: 0.7800 (pp) REVERT: A 468 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7233 (mm) REVERT: A 661 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7634 (tm-30) REVERT: B 515 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.5844 (p90) REVERT: B 933 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8686 (mtpp) REVERT: C 41 LYS cc_start: 0.7906 (mttt) cc_final: 0.7625 (mmmt) REVERT: C 53 ASP cc_start: 0.7768 (m-30) cc_final: 0.7426 (m-30) REVERT: C 94 SER cc_start: 0.7175 (m) cc_final: 0.6911 (p) REVERT: C 177 MET cc_start: 0.2665 (ttt) cc_final: 0.2291 (ttt) REVERT: C 900 MET cc_start: 0.9036 (mmm) cc_final: 0.8526 (mtt) REVERT: D 3 GLN cc_start: 0.4489 (pm20) cc_final: 0.3769 (pp30) REVERT: E 4 MET cc_start: 0.1855 (tmm) cc_final: 0.1542 (ppp) outliers start: 47 outliers final: 38 residues processed: 234 average time/residue: 0.4617 time to fit residues: 182.9135 Evaluate side-chains 233 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 132 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 348 optimal weight: 10.0000 chunk 233 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 245 optimal weight: 6.9990 chunk 226 optimal weight: 0.3980 chunk 72 optimal weight: 3.9990 chunk 355 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 146 HIS C 544 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.122008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.093906 restraints weight = 90654.263| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.45 r_work: 0.3445 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 28877 Z= 0.183 Angle : 0.628 59.200 39309 Z= 0.354 Chirality : 0.046 0.908 4424 Planarity : 0.004 0.063 5084 Dihedral : 3.875 20.279 3874 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.36 % Allowed : 13.86 % Favored : 84.78 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3565 helix: 1.74 (0.21), residues: 659 sheet: -0.24 (0.17), residues: 952 loop : -1.14 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.154 0.003 TRP A 886 HIS 0.002 0.001 HIS C1058 PHE 0.018 0.001 PHE A 238 TYR 0.108 0.002 TYR A 904 ARG 0.010 0.000 ARG C 319 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 971) hydrogen bonds : angle 4.74460 ( 2718) SS BOND : bond 0.00276 ( 43) SS BOND : angle 1.12167 ( 86) covalent geometry : bond 0.00406 (28834) covalent geometry : angle 0.62673 (39223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16934.88 seconds wall clock time: 294 minutes 56.64 seconds (17696.64 seconds total)