Starting phenix.real_space_refine on Tue Jun 24 18:41:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wcz_32430/06_2025/7wcz_32430.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wcz_32430/06_2025/7wcz_32430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wcz_32430/06_2025/7wcz_32430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wcz_32430/06_2025/7wcz_32430.map" model { file = "/net/cci-nas-00/data/ceres_data/7wcz_32430/06_2025/7wcz_32430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wcz_32430/06_2025/7wcz_32430.cif" } resolution = 3.5 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= 0.095 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 130 5.16 5 C 18286 2.51 5 N 4770 2.21 5 O 5493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 193 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28679 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1025} Chain breaks: 6 Chain: "a" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1627 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "b" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1690 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 8 Chain: "C" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 8 Time building chain proxies: 15.92, per 1000 atoms: 0.56 Number of scatterers: 28679 At special positions: 0 Unit cell: (147.555, 160.671, 280.901, 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 130 16.00 O 5493 8.00 N 4770 7.00 C 18286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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 a 22 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 199 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 94 " distance=2.03 Simple disulfide: pdb=" SG CYS b 139 " - pdb=" SG CYS b 199 " 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 379 " - pdb=" SG CYS B 432 " 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=1.52 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 379 " - pdb=" SG CYS C 432 " 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=2.04 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 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: 5.58 Conformation dependent library (CDL) restraints added in 3.4 seconds 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6872 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 59 sheets defined 20.3% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.531A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.793A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.553A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) 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 780 removed outlier: 3.688A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.586A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.561A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.578A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.783A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 3.986A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 65 removed outlier: 3.822A pdb=" N LYS a 65 " --> pdb=" O GLN a 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 62 through 65' Processing helix chain 'a' and resid 87 through 91 removed outlier: 3.880A pdb=" N SER a 91 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'b' and resid 126 through 131 removed outlier: 4.348A pdb=" N LEU b 130 " --> pdb=" O SER b 126 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR b 131 " --> pdb=" O SER b 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 126 through 131' Processing helix chain 'b' and resid 188 through 193 removed outlier: 3.535A pdb=" N GLU b 192 " --> pdb=" O LYS b 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.561A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.570A pdb=" N TYR B 505 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 506' Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.795A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.316A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 780 removed outlier: 3.528A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.581A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 removed outlier: 3.526A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.586A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 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: 3.736A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.516A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 4.028A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1160 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.562A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.569A pdb=" N TYR C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 506' Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.794A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.316A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 4.071A 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 780 removed outlier: 3.527A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.580A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 removed outlier: 3.526A pdb=" N PHE C 855 " --> pdb=" O CYS C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.585A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 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: 3.736A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.517A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1032 removed outlier: 4.029A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1160 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.184A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.432A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 6.805A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.200A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 142 removed outlier: 7.635A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.476A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.525A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.814A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.845A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.178A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.618A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 653 through 655 removed outlier: 5.969A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.562A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.865A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'a' and resid 3 through 6 removed outlier: 3.574A pdb=" N GLN a 3 " --> pdb=" O SER a 25 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL a 18 " --> pdb=" O PHE a 83 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR a 78 " --> pdb=" O ASP a 73 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU a 82 " --> pdb=" O THR a 69 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR a 69 " --> pdb=" O GLU a 82 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'a' and resid 10 through 12 removed outlier: 3.604A pdb=" N GLU a 10 " --> pdb=" O LEU a 112 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR a 114 " --> pdb=" O GLU a 10 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL a 12 " --> pdb=" O THR a 114 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL a 113 " --> pdb=" O ALA a 92 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA a 92 " --> pdb=" O VAL a 113 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR a 33 " --> pdb=" O ASP a 99 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET a 34 " --> pdb=" O GLY a 50 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP a 36 " --> pdb=" O ILE a 48 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP a 57 " --> pdb=" O ASN a 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'a' and resid 10 through 12 removed outlier: 3.604A pdb=" N GLU a 10 " --> pdb=" O LEU a 112 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR a 114 " --> pdb=" O GLU a 10 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL a 12 " --> pdb=" O THR a 114 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL a 113 " --> pdb=" O ALA a 92 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA a 92 " --> pdb=" O VAL a 113 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 124 through 128 removed outlier: 4.009A pdb=" N GLY a 143 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS a 144 " --> pdb=" O SER a 183 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER a 183 " --> pdb=" O CYS a 144 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY a 148 " --> pdb=" O TYR a 179 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 124 through 128 removed outlier: 4.009A pdb=" N GLY a 143 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS a 144 " --> pdb=" O SER a 183 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER a 183 " --> pdb=" O CYS a 144 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY a 148 " --> pdb=" O TYR a 179 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'a' and resid 155 through 158 removed outlier: 3.759A pdb=" N VAL a 197 " --> pdb=" O ILE a 214 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b' and resid 4 through 7 removed outlier: 3.741A pdb=" N THR b 22 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 10 through 12 removed outlier: 6.889A pdb=" N LEU b 11 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU b 39 " --> pdb=" O TYR b 55 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR b 55 " --> pdb=" O LEU b 39 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP b 41 " --> pdb=" O LEU b 53 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 30 through 31 removed outlier: 3.637A pdb=" N LYS b 36 " --> pdb=" O TYR b 31 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'b' and resid 122 through 123 removed outlier: 3.924A pdb=" N PHE b 123 " --> pdb=" O VAL b 138 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL b 138 " --> pdb=" O PHE b 123 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR b 178 " --> pdb=" O ASN b 143 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'b' and resid 158 through 159 removed outlier: 3.872A pdb=" N ASN b 150 " --> pdb=" O THR b 202 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.166A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.766A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.646A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.954A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.814A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.572A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 357 through 361 removed outlier: 3.672A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR B 393 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 423 through 424 removed outlier: 4.014A pdb=" N GLU B 465 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.236A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AE5, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.674A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.846A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.167A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.646A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.954A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.813A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 311 through 316 removed outlier: 5.486A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 357 through 361 removed outlier: 3.672A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR C 393 " --> pdb=" O ASN C 360 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 423 through 424 removed outlier: 4.014A pdb=" N GLU C 465 " --> pdb=" O LYS C 424 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.236A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AG2, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.675A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG5, first strand: chain 'C' and resid 1094 through 1097 1015 hydrogen bonds defined for protein. 2838 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: 12.48 Time building geometry restraints manager: 6.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.40: 12224 1.40 - 1.65: 16957 1.65 - 1.90: 165 1.90 - 2.15: 1 2.15 - 2.40: 1 Bond restraints: 29348 Sorted by residual: bond pdb=" C SER B 325 " pdb=" N ILE B 326 " ideal model delta sigma weight residual 1.329 2.403 -1.073 1.37e-02 5.33e+03 6.14e+03 bond pdb=" C LEU B 585 " pdb=" N ASP B 586 " ideal model delta sigma weight residual 1.328 2.005 -0.677 1.44e-02 4.82e+03 2.21e+03 bond pdb=" C VAL B 595 " pdb=" N SER B 596 " ideal model delta sigma weight residual 1.330 1.154 0.176 1.45e-02 4.76e+03 1.47e+02 bond pdb=" C THR B 315 " pdb=" N SER B 316 " ideal model delta sigma weight residual 1.331 1.261 0.070 1.39e-02 5.18e+03 2.51e+01 bond pdb=" C GLN A1142 " pdb=" N PRO A1143 " ideal model delta sigma weight residual 1.337 1.383 -0.047 1.06e-02 8.90e+03 1.93e+01 ... (remaining 29343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 39799 3.96 - 7.91: 105 7.91 - 11.87: 10 11.87 - 15.83: 4 15.83 - 19.79: 1 Bond angle restraints: 39919 Sorted by residual: angle pdb=" C LEU B 585 " pdb=" N ASP B 586 " pdb=" CA ASP B 586 " ideal model delta sigma weight residual 122.07 102.28 19.79 2.01e+00 2.48e-01 9.69e+01 angle pdb=" C SER B 325 " pdb=" N ILE B 326 " pdb=" CA ILE B 326 " ideal model delta sigma weight residual 123.11 110.46 12.65 1.36e+00 5.41e-01 8.65e+01 angle pdb=" O SER B 325 " pdb=" C SER B 325 " pdb=" N ILE B 326 " ideal model delta sigma weight residual 123.27 133.71 -10.44 1.18e+00 7.18e-01 7.83e+01 angle pdb=" CA SER B 325 " pdb=" C SER B 325 " pdb=" N ILE B 326 " ideal model delta sigma weight residual 116.37 105.96 10.41 1.19e+00 7.06e-01 7.65e+01 angle pdb=" O LEU B 585 " pdb=" C LEU B 585 " pdb=" N ASP B 586 " ideal model delta sigma weight residual 123.21 132.09 -8.88 1.27e+00 6.20e-01 4.89e+01 ... (remaining 39914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.29: 16818 26.29 - 52.58: 580 52.58 - 78.87: 58 78.87 - 105.16: 10 105.16 - 131.45: 2 Dihedral angle restraints: 17468 sinusoidal: 6788 harmonic: 10680 Sorted by residual: dihedral pdb=" CA CYS C 361 " pdb=" C CYS C 361 " pdb=" N VAL C 362 " pdb=" CA VAL C 362 " ideal model delta harmonic sigma weight residual 180.00 48.55 131.45 0 5.00e+00 4.00e-02 6.91e+02 dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 48.57 131.43 0 5.00e+00 4.00e-02 6.91e+02 dihedral pdb=" CB CYS b 139 " pdb=" SG CYS b 139 " pdb=" SG CYS b 199 " pdb=" CB CYS b 199 " ideal model delta sinusoidal sigma weight residual 93.00 175.69 -82.69 1 1.00e+01 1.00e-02 8.38e+01 ... (remaining 17465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3853 0.066 - 0.131: 605 0.131 - 0.197: 40 0.197 - 0.262: 7 0.262 - 0.328: 1 Chirality restraints: 4506 Sorted by residual: chirality pdb=" CB ILE b 155 " pdb=" CA ILE b 155 " pdb=" CG1 ILE b 155 " pdb=" CG2 ILE b 155 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ALA b 114 " pdb=" N ALA b 114 " pdb=" C ALA b 114 " pdb=" CB ALA b 114 " both_signs ideal model delta sigma weight residual False 2.48 2.74 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB THR b 119 " pdb=" CA THR b 119 " pdb=" OG1 THR b 119 " pdb=" CG2 THR b 119 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4503 not shown) Planarity restraints: 5163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 315 " 0.032 2.00e-02 2.50e+03 6.92e-02 4.79e+01 pdb=" C THR B 315 " -0.120 2.00e-02 2.50e+03 pdb=" O THR B 315 " 0.046 2.00e-02 2.50e+03 pdb=" N SER B 316 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA a 117 " 0.032 2.00e-02 2.50e+03 6.34e-02 4.01e+01 pdb=" C ALA a 117 " -0.110 2.00e-02 2.50e+03 pdb=" O ALA a 117 " 0.042 2.00e-02 2.50e+03 pdb=" N ALA a 118 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG b 113 " -0.031 2.00e-02 2.50e+03 6.16e-02 3.80e+01 pdb=" C ARG b 113 " 0.107 2.00e-02 2.50e+03 pdb=" O ARG b 113 " -0.041 2.00e-02 2.50e+03 pdb=" N ALA b 114 " -0.035 2.00e-02 2.50e+03 ... (remaining 5160 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 254 2.64 - 3.21: 22770 3.21 - 3.77: 42266 3.77 - 4.34: 59444 4.34 - 4.90: 97579 Nonbonded interactions: 222313 Sorted by model distance: nonbonded pdb=" NE2 GLN B 787 " pdb=" OD1 ASN C 703 " model vdw 2.076 3.120 nonbonded pdb=" NE2 GLN B 787 " pdb=" O VAL C 701 " model vdw 2.126 3.120 nonbonded pdb=" NE2 GLN A 787 " pdb=" OD1 ASN B 703 " model vdw 2.140 3.120 nonbonded pdb=" NE2 GLN A 787 " pdb=" O VAL B 701 " model vdw 2.161 3.120 nonbonded pdb=" NE2 GLN A 895 " pdb=" OD1 ASN B1074 " model vdw 2.214 3.120 ... (remaining 222308 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 61.630 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 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 : 0.009 1.073 29387 Z= 0.585 Angle : 0.701 19.787 39997 Z= 0.422 Chirality : 0.047 0.328 4506 Planarity : 0.006 0.069 5163 Dihedral : 12.674 131.451 10479 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.12 % Allowed : 4.24 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.24 (0.11), residues: 3616 helix: -4.64 (0.05), residues: 654 sheet: -0.25 (0.16), residues: 827 loop : -2.18 (0.11), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 56 HIS 0.002 0.000 HIS B 146 PHE 0.014 0.001 PHE C 490 TYR 0.017 0.001 TYR A 380 ARG 0.004 0.000 ARG B 44 Details of bonding type rmsd hydrogen bonds : bond 0.30410 ( 1002) hydrogen bonds : angle 10.37910 ( 2838) SS BOND : bond 0.08153 ( 39) SS BOND : angle 1.80883 ( 78) covalent geometry : bond 0.00805 (29348) covalent geometry : angle 0.69662 (39919) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 782 time to evaluate : 3.585 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: A 541 PHE cc_start: 0.7212 (p90) cc_final: 0.6798 (p90) REVERT: A 985 ASP cc_start: 0.7725 (m-30) cc_final: 0.6699 (m-30) REVERT: A 1081 ILE cc_start: 0.8752 (mm) cc_final: 0.8527 (mm) REVERT: a 139 MET cc_start: 0.1435 (ppp) cc_final: 0.0361 (mpp) REVERT: b 30 LEU cc_start: 0.6263 (tt) cc_final: 0.5823 (tp) REVERT: b 31 TYR cc_start: -0.2336 (t80) cc_final: -0.2716 (t80) REVERT: b 56 TRP cc_start: 0.3300 (m100) cc_final: 0.2500 (m100) REVERT: b 98 TYR cc_start: 0.3419 (t80) cc_final: 0.2532 (t80) REVERT: b 174 LYS cc_start: 0.3687 (mmtt) cc_final: 0.3464 (ptmm) REVERT: B 326 ILE cc_start: 0.4591 (mm) cc_final: 0.4295 (mt) REVERT: B 902 MET cc_start: 0.7935 (mmm) cc_final: 0.7714 (mmt) REVERT: B 933 LYS cc_start: 0.8673 (mttt) cc_final: 0.8366 (pttp) REVERT: C 316 SER cc_start: 0.8278 (p) cc_final: 0.8034 (p) REVERT: C 468 ILE cc_start: 0.4870 (pt) cc_final: 0.4586 (pt) REVERT: C 585 LEU cc_start: 0.5332 (mt) cc_final: 0.4939 (mt) REVERT: C 791 THR cc_start: 0.7130 (m) cc_final: 0.6856 (p) REVERT: C 902 MET cc_start: 0.8255 (mmm) cc_final: 0.8029 (mmt) REVERT: C 978 ASN cc_start: 0.8671 (m-40) cc_final: 0.8320 (p0) outliers start: 4 outliers final: 1 residues processed: 786 average time/residue: 0.4227 time to fit residues: 517.4292 Evaluate side-chains 354 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 284 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 211 optimal weight: 0.9990 chunk 329 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 149 ASN A 448 ASN A 450 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 644 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1048 HIS A1106 GLN a 62 GLN b 171 GLN B 164 ASN B 414 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 914 ASN B 955 ASN B1048 HIS B1106 GLN C 49 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 914 ASN C1010 GLN C1048 HIS C1101 HIS C1106 GLN C1119 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.180406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.143269 restraints weight = 78008.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.143573 restraints weight = 47722.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.144736 restraints weight = 30929.211| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29387 Z= 0.165 Angle : 0.621 8.741 39997 Z= 0.335 Chirality : 0.046 0.191 4506 Planarity : 0.005 0.063 5163 Dihedral : 4.596 54.264 3925 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.43 % Allowed : 12.58 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.65 (0.12), residues: 3620 helix: -1.13 (0.16), residues: 692 sheet: 0.29 (0.17), residues: 818 loop : -1.71 (0.11), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 64 HIS 0.006 0.001 HIS C 49 PHE 0.027 0.002 PHE A 135 TYR 0.023 0.002 TYR B 160 ARG 0.012 0.001 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.05381 ( 1002) hydrogen bonds : angle 6.20574 ( 2838) SS BOND : bond 0.00411 ( 39) SS BOND : angle 2.43845 ( 78) covalent geometry : bond 0.00361 (29348) covalent geometry : angle 0.61251 (39919) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 394 time to evaluate : 2.921 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 177 MET cc_start: 0.2661 (ttm) cc_final: 0.2147 (tmm) REVERT: A 380 TYR cc_start: 0.3469 (OUTLIER) cc_final: 0.3260 (m-10) REVERT: A 541 PHE cc_start: 0.7403 (p90) cc_final: 0.7188 (p90) REVERT: A 608 VAL cc_start: 0.8044 (t) cc_final: 0.7767 (p) REVERT: A 697 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6947 (mtt) REVERT: a 19 LYS cc_start: 0.5891 (mttt) cc_final: 0.5449 (ttpp) REVERT: a 139 MET cc_start: 0.1711 (ppp) cc_final: 0.0432 (mpp) REVERT: b 30 LEU cc_start: 0.5741 (tt) cc_final: 0.5394 (tt) REVERT: b 31 TYR cc_start: -0.2717 (t80) cc_final: -0.2993 (t80) REVERT: b 98 TYR cc_start: 0.3712 (t80) cc_final: 0.2763 (t80) REVERT: B 153 MET cc_start: 0.0784 (pmm) cc_final: 0.0042 (pmm) REVERT: B 158 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6182 (mmm160) REVERT: C 200 TYR cc_start: 0.7505 (m-80) cc_final: 0.7181 (m-80) REVERT: C 228 ASP cc_start: 0.7209 (t0) cc_final: 0.6839 (t0) REVERT: C 791 THR cc_start: 0.7507 (m) cc_final: 0.7248 (p) REVERT: C 938 LEU cc_start: 0.8327 (mt) cc_final: 0.8039 (mt) REVERT: C 1142 GLN cc_start: 0.7457 (tp40) cc_final: 0.7246 (tp40) outliers start: 78 outliers final: 44 residues processed: 455 average time/residue: 0.3764 time to fit residues: 278.6562 Evaluate side-chains 327 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 171 optimal weight: 10.0000 chunk 249 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 345 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 179 optimal weight: 2.9990 chunk 316 optimal weight: 0.0770 chunk 33 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 195 optimal weight: 0.0470 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 751 ASN A 787 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 787 GLN B1088 HIS B1119 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.178972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.141372 restraints weight = 78357.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.143190 restraints weight = 41862.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.143838 restraints weight = 23955.080| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 29387 Z= 0.110 Angle : 0.539 10.616 39997 Z= 0.286 Chirality : 0.043 0.175 4506 Planarity : 0.004 0.068 5163 Dihedral : 4.345 39.831 3925 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.24 % Allowed : 15.07 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.79 (0.13), residues: 3620 helix: 0.71 (0.20), residues: 696 sheet: 0.49 (0.17), residues: 818 loop : -1.44 (0.12), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 886 HIS 0.004 0.001 HIS A 655 PHE 0.034 0.001 PHE A 643 TYR 0.017 0.001 TYR A 265 ARG 0.007 0.000 ARG C 905 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 1002) hydrogen bonds : angle 5.50804 ( 2838) SS BOND : bond 0.00327 ( 39) SS BOND : angle 2.18466 ( 78) covalent geometry : bond 0.00241 (29348) covalent geometry : angle 0.53076 (39919) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 315 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8560 (t) cc_final: 0.8254 (t) REVERT: A 177 MET cc_start: 0.2739 (ttm) cc_final: 0.2242 (tmm) REVERT: A 380 TYR cc_start: 0.3513 (OUTLIER) cc_final: 0.3207 (m-10) REVERT: A 541 PHE cc_start: 0.7381 (p90) cc_final: 0.7158 (p90) REVERT: A 608 VAL cc_start: 0.8023 (t) cc_final: 0.7770 (p) REVERT: A 900 MET cc_start: 0.7678 (mtm) cc_final: 0.7264 (mtp) REVERT: a 139 MET cc_start: 0.2211 (ppp) cc_final: 0.0847 (mpp) REVERT: b 30 LEU cc_start: 0.5763 (tt) cc_final: 0.5292 (tt) REVERT: b 31 TYR cc_start: -0.2554 (t80) cc_final: -0.2948 (t80) REVERT: b 54 ILE cc_start: 0.4001 (mp) cc_final: 0.3752 (mt) REVERT: b 98 TYR cc_start: 0.3911 (t80) cc_final: 0.2896 (t80) REVERT: B 153 MET cc_start: 0.0665 (pmm) cc_final: 0.0159 (pmm) REVERT: B 158 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6360 (mmm160) REVERT: B 904 TYR cc_start: 0.6266 (t80) cc_final: 0.5935 (t80) REVERT: C 177 MET cc_start: 0.0425 (tpt) cc_final: 0.0029 (tpt) REVERT: C 200 TYR cc_start: 0.7562 (m-80) cc_final: 0.7168 (m-80) REVERT: C 480 CYS cc_start: 0.4253 (OUTLIER) cc_final: 0.3738 (t) REVERT: C 585 LEU cc_start: 0.6468 (mt) cc_final: 0.6259 (mt) REVERT: C 791 THR cc_start: 0.7719 (m) cc_final: 0.7381 (p) REVERT: C 938 LEU cc_start: 0.8157 (mt) cc_final: 0.7871 (mt) outliers start: 72 outliers final: 43 residues processed: 370 average time/residue: 0.3578 time to fit residues: 226.7557 Evaluate side-chains 312 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 266 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 197 VAL Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 265 optimal weight: 7.9990 chunk 216 optimal weight: 0.5980 chunk 362 optimal weight: 0.5980 chunk 157 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 310 optimal weight: 0.0970 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 506 GLN C 655 HIS C 969 ASN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.177772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.143685 restraints weight = 78249.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.143508 restraints weight = 48804.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.143527 restraints weight = 32329.687| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 29387 Z= 0.114 Angle : 0.532 11.962 39997 Z= 0.281 Chirality : 0.043 0.292 4506 Planarity : 0.004 0.069 5163 Dihedral : 4.234 38.808 3924 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.65 % Allowed : 16.19 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.47 (0.13), residues: 3620 helix: 1.25 (0.20), residues: 704 sheet: 0.50 (0.17), residues: 848 loop : -1.27 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 886 HIS 0.003 0.001 HIS A 519 PHE 0.023 0.001 PHE B 135 TYR 0.013 0.001 TYR A 265 ARG 0.004 0.000 ARG C 905 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 1002) hydrogen bonds : angle 5.17468 ( 2838) SS BOND : bond 0.00458 ( 39) SS BOND : angle 2.49167 ( 78) covalent geometry : bond 0.00258 (29348) covalent geometry : angle 0.52051 (39919) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 296 time to evaluate : 3.166 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 608 VAL cc_start: 0.8070 (t) cc_final: 0.7826 (p) REVERT: A 774 GLN cc_start: 0.8340 (mp10) cc_final: 0.7923 (mp10) REVERT: A 900 MET cc_start: 0.8015 (mtm) cc_final: 0.7451 (mtp) REVERT: a 81 MET cc_start: 0.0559 (tmm) cc_final: 0.0214 (tmm) REVERT: a 109 GLN cc_start: 0.5932 (pm20) cc_final: 0.5092 (tt0) REVERT: a 139 MET cc_start: 0.1907 (ppp) cc_final: 0.0477 (mpp) REVERT: b 30 LEU cc_start: 0.5833 (tt) cc_final: 0.5308 (tt) REVERT: b 54 ILE cc_start: 0.4538 (mp) cc_final: 0.4334 (mt) REVERT: b 98 TYR cc_start: 0.4086 (t80) cc_final: 0.2669 (t80) REVERT: B 153 MET cc_start: 0.0680 (pmm) cc_final: 0.0351 (pmm) REVERT: B 158 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.6354 (mmm160) REVERT: B 612 TYR cc_start: 0.8444 (m-80) cc_final: 0.8194 (m-10) REVERT: B 731 MET cc_start: 0.8819 (ptm) cc_final: 0.8604 (ptp) REVERT: B 739 THR cc_start: 0.8265 (m) cc_final: 0.7942 (p) REVERT: B 918 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7181 (mp0) REVERT: C 200 TYR cc_start: 0.7585 (m-80) cc_final: 0.7185 (m-80) outliers start: 85 outliers final: 58 residues processed: 364 average time/residue: 0.3394 time to fit residues: 209.8389 Evaluate side-chains 318 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 259 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 83 PHE Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 93 TYR Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 151 optimal weight: 0.5980 chunk 268 optimal weight: 5.9990 chunk 359 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 217 optimal weight: 0.0060 chunk 227 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 245 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 901 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 95 GLN B1119 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.171413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.136072 restraints weight = 76925.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.136487 restraints weight = 45364.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.135991 restraints weight = 31760.404| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 29387 Z= 0.192 Angle : 0.629 12.671 39997 Z= 0.335 Chirality : 0.046 0.220 4506 Planarity : 0.004 0.065 5163 Dihedral : 4.698 40.662 3924 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.92 % Allowed : 16.35 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.54 (0.13), residues: 3620 helix: 1.03 (0.20), residues: 732 sheet: 0.37 (0.17), residues: 862 loop : -1.24 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 886 HIS 0.008 0.001 HIS A 519 PHE 0.024 0.002 PHE b 123 TYR 0.020 0.002 TYR C 38 ARG 0.008 0.001 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 1002) hydrogen bonds : angle 5.28628 ( 2838) SS BOND : bond 0.00568 ( 39) SS BOND : angle 3.14032 ( 78) covalent geometry : bond 0.00441 (29348) covalent geometry : angle 0.61445 (39919) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 283 time to evaluate : 3.169 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 608 VAL cc_start: 0.8337 (t) cc_final: 0.8011 (p) REVERT: A 759 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7785 (t80) REVERT: A 900 MET cc_start: 0.8132 (mtm) cc_final: 0.7714 (mtp) REVERT: a 139 MET cc_start: 0.1843 (ppp) cc_final: 0.0701 (mpp) REVERT: b 30 LEU cc_start: 0.5960 (tt) cc_final: 0.5458 (tt) REVERT: b 31 TYR cc_start: -0.2430 (t80) cc_final: -0.2993 (t80) REVERT: b 98 TYR cc_start: 0.4023 (t80) cc_final: 0.2526 (t80) REVERT: B 102 ARG cc_start: 0.2850 (OUTLIER) cc_final: 0.0853 (mpt180) REVERT: B 153 MET cc_start: 0.0978 (pmm) cc_final: 0.0567 (pmm) REVERT: B 158 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6617 (mmm160) REVERT: C 177 MET cc_start: 0.1057 (tpt) cc_final: 0.0805 (tpt) REVERT: C 200 TYR cc_start: 0.7746 (m-80) cc_final: 0.7424 (m-80) REVERT: C 759 PHE cc_start: 0.7503 (t80) cc_final: 0.7206 (t80) REVERT: C 974 SER cc_start: 0.8805 (t) cc_final: 0.8428 (p) outliers start: 126 outliers final: 78 residues processed: 386 average time/residue: 0.3670 time to fit residues: 242.5169 Evaluate side-chains 322 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 241 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 83 PHE Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 30 optimal weight: 0.0370 chunk 279 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 19 optimal weight: 0.0060 chunk 59 optimal weight: 0.4980 chunk 342 optimal weight: 3.9990 chunk 315 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 overall best weight: 1.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 856 ASN A 872 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.170532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.135579 restraints weight = 77165.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.135671 restraints weight = 48088.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.135582 restraints weight = 31920.440| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29387 Z= 0.161 Angle : 0.580 12.422 39997 Z= 0.306 Chirality : 0.045 0.163 4506 Planarity : 0.004 0.069 5163 Dihedral : 4.604 39.575 3924 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.24 % Allowed : 17.94 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.47 (0.13), residues: 3620 helix: 1.21 (0.20), residues: 728 sheet: 0.43 (0.17), residues: 835 loop : -1.24 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 886 HIS 0.006 0.001 HIS A 146 PHE 0.031 0.002 PHE C 643 TYR 0.017 0.002 TYR A 505 ARG 0.007 0.001 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 1002) hydrogen bonds : angle 5.12074 ( 2838) SS BOND : bond 0.00429 ( 39) SS BOND : angle 2.09777 ( 78) covalent geometry : bond 0.00372 (29348) covalent geometry : angle 0.57356 (39919) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 261 time to evaluate : 3.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 PHE cc_start: 0.7500 (p90) cc_final: 0.7097 (p90) REVERT: A 608 VAL cc_start: 0.8255 (t) cc_final: 0.7979 (p) REVERT: A 759 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7561 (t80) REVERT: A 900 MET cc_start: 0.8058 (mtm) cc_final: 0.7660 (mtp) REVERT: a 83 PHE cc_start: 0.0848 (OUTLIER) cc_final: 0.0611 (m-10) REVERT: a 139 MET cc_start: 0.1869 (ppp) cc_final: 0.0646 (mpp) REVERT: b 30 LEU cc_start: 0.6450 (tt) cc_final: 0.6199 (tt) REVERT: B 153 MET cc_start: 0.1319 (pmm) cc_final: 0.0939 (pmm) REVERT: B 158 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.6437 (mtp85) REVERT: B 189 LEU cc_start: 0.7731 (tp) cc_final: 0.7523 (tp) REVERT: C 177 MET cc_start: 0.1191 (tpt) cc_final: 0.0853 (tpt) REVERT: C 200 TYR cc_start: 0.7668 (m-80) cc_final: 0.7446 (m-80) REVERT: C 974 SER cc_start: 0.8713 (t) cc_final: 0.8166 (p) outliers start: 104 outliers final: 74 residues processed: 350 average time/residue: 0.3394 time to fit residues: 204.3536 Evaluate side-chains 298 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 221 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 83 PHE Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 136 THR Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 93 TYR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 93 optimal weight: 0.6980 chunk 276 optimal weight: 0.8980 chunk 337 optimal weight: 0.6980 chunk 193 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 343 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 755 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.171184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.135862 restraints weight = 76743.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.136481 restraints weight = 42553.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.136521 restraints weight = 29630.723| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29387 Z= 0.116 Angle : 0.538 8.569 39997 Z= 0.283 Chirality : 0.043 0.172 4506 Planarity : 0.004 0.068 5163 Dihedral : 4.402 39.073 3924 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.71 % Allowed : 18.87 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.31 (0.14), residues: 3620 helix: 1.39 (0.20), residues: 744 sheet: 0.52 (0.17), residues: 833 loop : -1.16 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 886 HIS 0.003 0.001 HIS C 207 PHE 0.021 0.001 PHE B1148 TYR 0.019 0.001 TYR A 380 ARG 0.004 0.000 ARG C 815 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 1002) hydrogen bonds : angle 4.97547 ( 2838) SS BOND : bond 0.00377 ( 39) SS BOND : angle 1.81124 ( 78) covalent geometry : bond 0.00263 (29348) covalent geometry : angle 0.53230 (39919) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 253 time to evaluate : 3.459 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 541 PHE cc_start: 0.7525 (p90) cc_final: 0.7183 (p90) REVERT: A 608 VAL cc_start: 0.8192 (t) cc_final: 0.7893 (p) REVERT: A 661 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7102 (tm-30) REVERT: A 759 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7600 (t80) REVERT: A 900 MET cc_start: 0.7989 (mtm) cc_final: 0.7593 (mtp) REVERT: a 139 MET cc_start: 0.1951 (ppp) cc_final: 0.0785 (mpp) REVERT: B 102 ARG cc_start: 0.2672 (OUTLIER) cc_final: 0.0484 (mpt180) REVERT: B 153 MET cc_start: 0.1522 (pmm) cc_final: 0.1163 (pmm) REVERT: B 158 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6581 (mtp85) REVERT: B 189 LEU cc_start: 0.7744 (tp) cc_final: 0.7527 (tp) REVERT: B 523 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7337 (p) REVERT: B 969 ASN cc_start: 0.8579 (m-40) cc_final: 0.8353 (m110) REVERT: C 177 MET cc_start: 0.0966 (tpt) cc_final: 0.0626 (tpt) REVERT: C 200 TYR cc_start: 0.7676 (m-80) cc_final: 0.7461 (m-80) REVERT: C 974 SER cc_start: 0.8517 (t) cc_final: 0.8112 (p) outliers start: 87 outliers final: 66 residues processed: 322 average time/residue: 0.3899 time to fit residues: 213.7973 Evaluate side-chains 299 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 229 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 81 MET Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 93 TYR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 3 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 337 optimal weight: 0.8980 chunk 335 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 361 optimal weight: 0.8980 chunk 325 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 914 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.170338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.135423 restraints weight = 77270.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.135186 restraints weight = 44364.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.135743 restraints weight = 31758.429| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.6199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29387 Z= 0.130 Angle : 0.552 8.963 39997 Z= 0.290 Chirality : 0.044 0.157 4506 Planarity : 0.004 0.083 5163 Dihedral : 4.431 38.906 3924 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.80 % Allowed : 19.12 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.28 (0.14), residues: 3620 helix: 1.41 (0.20), residues: 744 sheet: 0.54 (0.17), residues: 832 loop : -1.15 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 886 HIS 0.004 0.001 HIS C 207 PHE 0.032 0.001 PHE A 429 TYR 0.028 0.001 TYR a 179 ARG 0.005 0.000 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 1002) hydrogen bonds : angle 4.95029 ( 2838) SS BOND : bond 0.00344 ( 39) SS BOND : angle 2.07192 ( 78) covalent geometry : bond 0.00297 (29348) covalent geometry : angle 0.54526 (39919) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 244 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 PHE cc_start: 0.7649 (p90) cc_final: 0.7376 (p90) REVERT: A 608 VAL cc_start: 0.8257 (t) cc_final: 0.7965 (p) REVERT: A 661 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7108 (tm-30) REVERT: A 900 MET cc_start: 0.8032 (mtm) cc_final: 0.7627 (mtp) REVERT: A 1155 TYR cc_start: 0.1343 (t80) cc_final: 0.1123 (m-80) REVERT: a 139 MET cc_start: 0.1303 (ppp) cc_final: 0.0275 (mpp) REVERT: a 179 TYR cc_start: 0.4242 (OUTLIER) cc_final: 0.3576 (t80) REVERT: B 102 ARG cc_start: 0.3008 (OUTLIER) cc_final: 0.0671 (mpt180) REVERT: B 153 MET cc_start: 0.1484 (pmm) cc_final: 0.1259 (pmm) REVERT: B 158 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.6329 (mmm160) REVERT: B 189 LEU cc_start: 0.7673 (tp) cc_final: 0.7461 (tp) REVERT: B 523 THR cc_start: 0.7464 (OUTLIER) cc_final: 0.7216 (p) REVERT: B 559 PHE cc_start: 0.5501 (OUTLIER) cc_final: 0.2866 (m-80) REVERT: B 929 SER cc_start: 0.8304 (m) cc_final: 0.8042 (t) REVERT: B 955 ASN cc_start: 0.8195 (m-40) cc_final: 0.7951 (t0) REVERT: B 969 ASN cc_start: 0.8590 (m-40) cc_final: 0.8355 (m110) REVERT: C 177 MET cc_start: 0.1048 (tpt) cc_final: 0.0759 (tpt) REVERT: C 740 MET cc_start: 0.7032 (ttt) cc_final: 0.6513 (ttt) REVERT: C 974 SER cc_start: 0.8665 (t) cc_final: 0.8276 (p) REVERT: C 1010 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7834 (tp40) outliers start: 90 outliers final: 74 residues processed: 316 average time/residue: 0.3502 time to fit residues: 188.1517 Evaluate side-chains 303 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 224 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 81 MET Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 93 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 279 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 129 optimal weight: 0.1980 chunk 252 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 223 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN ** a 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1010 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 = 0.4466 r_free = 0.4466 target = 0.170739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.135193 restraints weight = 76854.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.136413 restraints weight = 40921.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.136640 restraints weight = 24672.697| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.6345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29387 Z= 0.117 Angle : 0.536 9.634 39997 Z= 0.281 Chirality : 0.043 0.154 4506 Planarity : 0.004 0.079 5163 Dihedral : 4.359 38.304 3924 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.83 % Allowed : 19.28 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.23 (0.14), residues: 3620 helix: 1.52 (0.20), residues: 744 sheet: 0.57 (0.17), residues: 839 loop : -1.15 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 886 HIS 0.004 0.001 HIS C 207 PHE 0.023 0.001 PHE B 106 TYR 0.014 0.001 TYR C1067 ARG 0.006 0.000 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 1002) hydrogen bonds : angle 4.89343 ( 2838) SS BOND : bond 0.00340 ( 39) SS BOND : angle 1.88653 ( 78) covalent geometry : bond 0.00266 (29348) covalent geometry : angle 0.52991 (39919) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 244 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 PHE cc_start: 0.7771 (p90) cc_final: 0.7567 (p90) REVERT: A 608 VAL cc_start: 0.8280 (t) cc_final: 0.7994 (p) REVERT: A 823 PHE cc_start: 0.8044 (t80) cc_final: 0.7702 (m-80) REVERT: A 900 MET cc_start: 0.8019 (mtm) cc_final: 0.7575 (mtp) REVERT: a 139 MET cc_start: 0.1043 (ppp) cc_final: 0.0171 (mpp) REVERT: a 179 TYR cc_start: 0.4084 (OUTLIER) cc_final: 0.3465 (t80) REVERT: B 102 ARG cc_start: 0.2934 (OUTLIER) cc_final: 0.0594 (mpt180) REVERT: B 153 MET cc_start: 0.1637 (pmm) cc_final: 0.1396 (pmm) REVERT: B 189 LEU cc_start: 0.7693 (tp) cc_final: 0.7483 (tp) REVERT: B 523 THR cc_start: 0.7457 (OUTLIER) cc_final: 0.7228 (p) REVERT: B 559 PHE cc_start: 0.5376 (OUTLIER) cc_final: 0.2745 (m-80) REVERT: B 929 SER cc_start: 0.8344 (m) cc_final: 0.8056 (t) REVERT: B 955 ASN cc_start: 0.8174 (m-40) cc_final: 0.7961 (t0) REVERT: C 177 MET cc_start: 0.0870 (tpt) cc_final: 0.0581 (tpt) REVERT: C 974 SER cc_start: 0.8588 (t) cc_final: 0.8259 (p) REVERT: C 1010 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7754 (tp40) REVERT: C 1014 ARG cc_start: 0.7648 (mtt180) cc_final: 0.7399 (mtm110) outliers start: 91 outliers final: 78 residues processed: 318 average time/residue: 0.3469 time to fit residues: 186.4190 Evaluate side-chains 304 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 222 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 81 MET Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 93 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 205 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 355 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 340 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 321 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 856 ASN ** a 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.168565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.133858 restraints weight = 76727.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.134634 restraints weight = 41363.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.134517 restraints weight = 27304.316| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.6614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29387 Z= 0.145 Angle : 0.574 10.849 39997 Z= 0.300 Chirality : 0.044 0.159 4506 Planarity : 0.004 0.084 5163 Dihedral : 4.498 38.525 3924 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.49 % Allowed : 19.68 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.28 (0.14), residues: 3620 helix: 1.45 (0.20), residues: 744 sheet: 0.50 (0.17), residues: 843 loop : -1.16 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 886 HIS 0.004 0.001 HIS C1064 PHE 0.025 0.002 PHE B 106 TYR 0.025 0.001 TYR A1155 ARG 0.019 0.001 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 1002) hydrogen bonds : angle 5.00165 ( 2838) SS BOND : bond 0.00364 ( 39) SS BOND : angle 1.87553 ( 78) covalent geometry : bond 0.00336 (29348) covalent geometry : angle 0.56890 (39919) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 244 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 608 VAL cc_start: 0.8329 (t) cc_final: 0.8032 (p) REVERT: A 661 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7166 (tm-30) REVERT: A 823 PHE cc_start: 0.8130 (t80) cc_final: 0.7754 (m-80) REVERT: A 900 MET cc_start: 0.8081 (mtm) cc_final: 0.7664 (mtp) REVERT: a 139 MET cc_start: 0.1101 (ppp) cc_final: 0.0255 (mpp) REVERT: a 179 TYR cc_start: 0.4205 (OUTLIER) cc_final: 0.3555 (t80) REVERT: B 102 ARG cc_start: 0.3036 (OUTLIER) cc_final: 0.0637 (mpt180) REVERT: B 153 MET cc_start: 0.1864 (pmm) cc_final: 0.1655 (pmm) REVERT: B 189 LEU cc_start: 0.7688 (tp) cc_final: 0.7456 (tp) REVERT: B 523 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.7250 (p) REVERT: B 559 PHE cc_start: 0.5473 (OUTLIER) cc_final: 0.2801 (m-80) REVERT: B 929 SER cc_start: 0.8369 (m) cc_final: 0.8087 (t) REVERT: C 177 MET cc_start: 0.0944 (tpt) cc_final: 0.0670 (tpt) REVERT: C 974 SER cc_start: 0.8714 (t) cc_final: 0.8454 (p) REVERT: C 1010 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7887 (tp40) outliers start: 80 outliers final: 68 residues processed: 309 average time/residue: 0.3985 time to fit residues: 209.0392 Evaluate side-chains 306 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 234 time to evaluate : 3.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 81 MET Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 250 optimal weight: 4.9990 chunk 202 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 332 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 360 optimal weight: 0.2980 chunk 205 optimal weight: 2.9990 chunk 349 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** a 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1005 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.169366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.135112 restraints weight = 76819.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.135714 restraints weight = 43479.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.135490 restraints weight = 29152.985| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29387 Z= 0.121 Angle : 0.549 11.201 39997 Z= 0.287 Chirality : 0.044 0.168 4506 Planarity : 0.004 0.087 5163 Dihedral : 4.444 37.489 3924 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.43 % Allowed : 19.90 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.22 (0.14), residues: 3620 helix: 1.60 (0.20), residues: 741 sheet: 0.50 (0.17), residues: 843 loop : -1.13 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 886 HIS 0.004 0.001 HIS C 207 PHE 0.047 0.001 PHE A 643 TYR 0.051 0.001 TYR B 160 ARG 0.007 0.000 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 1002) hydrogen bonds : angle 4.91773 ( 2838) SS BOND : bond 0.00331 ( 39) SS BOND : angle 1.73367 ( 78) covalent geometry : bond 0.00277 (29348) covalent geometry : angle 0.54378 (39919) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10529.58 seconds wall clock time: 183 minutes 45.80 seconds (11025.80 seconds total)