Starting phenix.real_space_refine on Fri Mar 6 05:58:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wcz_32430/03_2026/7wcz_32430.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wcz_32430/03_2026/7wcz_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wcz_32430/03_2026/7wcz_32430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wcz_32430/03_2026/7wcz_32430.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wcz_32430/03_2026/7wcz_32430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wcz_32430/03_2026/7wcz_32430.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.47, per 1000 atoms: 0.23 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: 2.44 Conformation dependent library (CDL) restraints added in 1.4 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: 1.35 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: 7.06 Time building geometry restraints manager: 3.35 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: 5.970 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: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 27.600 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.230 ------------------------------------------------------------------------------- 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 : 4.42 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (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 ARG 0.004 0.000 ARG B 44 TYR 0.017 0.001 TYR A 380 PHE 0.014 0.001 PHE C 490 TRP 0.009 0.001 TRP b 56 HIS 0.002 0.000 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00805 (29348) covalent geometry : angle 0.69662 (39919) SS BOND : bond 0.08153 ( 39) SS BOND : angle 1.80883 ( 78) hydrogen bonds : bond 0.30410 ( 1002) hydrogen bonds : angle 10.37910 ( 2838) *********************** 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 : 0.809 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: 0.6505 (m-30) REVERT: A 1081 ILE cc_start: 0.8752 (mm) cc_final: 0.8528 (mm) REVERT: a 139 MET cc_start: 0.1435 (ppp) cc_final: 0.0362 (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: -0.2714 (t80) REVERT: b 56 TRP cc_start: 0.3300 (m100) cc_final: 0.2506 (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: 0.4293 (mt) REVERT: B 902 MET cc_start: 0.7935 (mmm) cc_final: 0.7715 (mmt) REVERT: B 933 LYS cc_start: 0.8673 (mttt) cc_final: 0.8367 (pttp) REVERT: C 316 SER cc_start: 0.8278 (p) cc_final: 0.8037 (p) REVERT: C 468 ILE cc_start: 0.4870 (pt) cc_final: 0.4582 (pt) REVERT: C 585 LEU cc_start: 0.5332 (mt) cc_final: 0.4940 (mt) REVERT: C 791 THR cc_start: 0.7130 (m) cc_final: 0.6855 (p) REVERT: C 902 MET cc_start: 0.8255 (mmm) cc_final: 0.8031 (mmt) REVERT: C 978 ASN cc_start: 0.8671 (m-40) cc_final: 0.8321 (p0) outliers start: 4 outliers final: 1 residues processed: 786 average time/residue: 0.1917 time to fit residues: 235.1130 Evaluate side-chains 351 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 350 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 394 ASN A 448 ASN A 450 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 613 GLN A 751 ASN A 955 ASN A1048 HIS A1106 GLN a 62 GLN b 171 GLN B 164 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 856 ASN 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.181279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.144005 restraints weight = 78517.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.145107 restraints weight = 47950.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.145604 restraints weight = 26894.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.146170 restraints weight = 24196.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.146213 restraints weight = 21344.202| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29387 Z= 0.153 Angle : 0.621 9.797 39997 Z= 0.332 Chirality : 0.046 0.186 4506 Planarity : 0.005 0.061 5163 Dihedral : 4.580 52.856 3925 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.30 % Allowed : 12.49 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.12), residues: 3620 helix: -1.02 (0.17), residues: 691 sheet: 0.31 (0.17), residues: 820 loop : -1.69 (0.12), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 567 TYR 0.023 0.002 TYR B 160 PHE 0.029 0.002 PHE A 135 TRP 0.023 0.002 TRP C 64 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00333 (29348) covalent geometry : angle 0.61264 (39919) SS BOND : bond 0.00944 ( 39) SS BOND : angle 2.43200 ( 78) hydrogen bonds : bond 0.05082 ( 1002) hydrogen bonds : angle 6.19593 ( 2838) *********************** 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 477 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 403 time to evaluate : 0.990 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: 0.2494 (ttm) cc_final: 0.2010 (tmm) REVERT: A 380 TYR cc_start: 0.3359 (OUTLIER) cc_final: 0.3154 (m-10) REVERT: A 608 VAL cc_start: 0.7926 (t) cc_final: 0.7671 (p) REVERT: A 697 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6898 (mtt) REVERT: A 776 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8531 (tttp) REVERT: a 139 MET cc_start: 0.1714 (ppp) cc_final: 0.0431 (mpp) REVERT: b 30 LEU cc_start: 0.5769 (tt) cc_final: 0.5402 (tt) REVERT: b 31 TYR cc_start: -0.2674 (t80) cc_final: -0.2923 (t80) REVERT: b 98 TYR cc_start: 0.3665 (t80) cc_final: 0.2716 (t80) REVERT: B 153 MET cc_start: 0.0717 (pmm) cc_final: 0.0016 (pmm) REVERT: B 158 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.6304 (mmm160) REVERT: B 309 GLU cc_start: 0.7904 (pt0) cc_final: 0.7489 (pt0) REVERT: C 102 ARG cc_start: 0.0850 (ptp-170) cc_final: 0.0548 (ptp-170) REVERT: C 200 TYR cc_start: 0.7534 (m-80) cc_final: 0.7220 (m-80) REVERT: C 228 ASP cc_start: 0.7265 (t0) cc_final: 0.6857 (t0) REVERT: C 791 THR cc_start: 0.7461 (m) cc_final: 0.7185 (p) REVERT: C 938 LEU cc_start: 0.8312 (mt) cc_final: 0.8026 (mt) REVERT: C 1010 GLN cc_start: 0.7975 (tp-100) cc_final: 0.7549 (tp40) REVERT: C 1014 ARG cc_start: 0.7711 (mtt180) cc_final: 0.7415 (mtm-85) REVERT: C 1156 PHE cc_start: -0.3044 (m-80) cc_final: -0.3325 (m-80) outliers start: 74 outliers final: 40 residues processed: 461 average time/residue: 0.1712 time to fit residues: 129.1550 Evaluate side-chains 329 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 286 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 197 VAL 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 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN 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 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 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 64 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 358 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 288 optimal weight: 0.1980 chunk 102 optimal weight: 2.9990 chunk 339 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 A 655 HIS A 787 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 GLN b 95 GLN ** 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 C 978 ASN C1002 GLN C1011 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.174830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.139616 restraints weight = 77957.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.139217 restraints weight = 49979.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.139012 restraints weight = 35065.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.139325 restraints weight = 31043.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.139594 restraints weight = 27109.191| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 29387 Z= 0.175 Angle : 0.609 10.881 39997 Z= 0.325 Chirality : 0.045 0.191 4506 Planarity : 0.004 0.071 5163 Dihedral : 4.628 40.788 3925 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.55 % Allowed : 15.17 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 3620 helix: 0.57 (0.20), residues: 705 sheet: 0.36 (0.17), residues: 844 loop : -1.48 (0.12), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 44 TYR 0.018 0.002 TYR A 380 PHE 0.029 0.002 PHE A 643 TRP 0.016 0.002 TRP a 158 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00400 (29348) covalent geometry : angle 0.60070 (39919) SS BOND : bond 0.00439 ( 39) SS BOND : angle 2.35935 ( 78) hydrogen bonds : bond 0.04852 ( 1002) hydrogen bonds : angle 5.58472 ( 2838) *********************** 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 419 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 305 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 608 VAL cc_start: 0.8251 (t) cc_final: 0.7924 (p) REVERT: A 900 MET cc_start: 0.7869 (mpp) cc_final: 0.7598 (mtp) REVERT: a 139 MET cc_start: 0.2355 (ppp) cc_final: 0.0916 (mpp) REVERT: B 153 MET cc_start: 0.0784 (pmm) cc_final: 0.0329 (pmm) REVERT: B 158 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6573 (mmm160) REVERT: B 740 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6379 (mtt) REVERT: B 904 TYR cc_start: 0.6684 (t80) cc_final: 0.6383 (t80) REVERT: B 1146 ASP cc_start: 0.6582 (m-30) cc_final: 0.6368 (m-30) REVERT: C 177 MET cc_start: 0.0729 (tpt) cc_final: 0.0336 (tpt) REVERT: C 200 TYR cc_start: 0.7551 (m-80) cc_final: 0.7123 (m-80) REVERT: C 480 CYS cc_start: 0.3849 (OUTLIER) cc_final: 0.3317 (t) REVERT: C 938 LEU cc_start: 0.8399 (mt) cc_final: 0.8153 (mt) REVERT: C 974 SER cc_start: 0.8625 (t) cc_final: 0.8425 (p) REVERT: C 1010 GLN cc_start: 0.8273 (tp-100) cc_final: 0.8073 (tp40) REVERT: C 1142 GLN cc_start: 0.7450 (tp40) cc_final: 0.7242 (tp40) outliers start: 114 outliers final: 70 residues processed: 393 average time/residue: 0.1530 time to fit residues: 102.7813 Evaluate side-chains 328 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 255 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 135 PHE 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 365 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 872 GLN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1029 MET 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 124 SER 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 3 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 370 ASN 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 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP 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 980 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1106 GLN 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 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 605 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 82 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 177 optimal weight: 0.5980 chunk 218 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 207 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A1005 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 935 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 655 HIS C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.172440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.137371 restraints weight = 77035.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.136705 restraints weight = 43925.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.137172 restraints weight = 31453.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.137584 restraints weight = 25932.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.137763 restraints weight = 24102.701| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29387 Z= 0.160 Angle : 0.581 9.648 39997 Z= 0.309 Chirality : 0.045 0.176 4506 Planarity : 0.004 0.069 5163 Dihedral : 4.598 40.404 3924 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.77 % Allowed : 16.63 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 3620 helix: 0.98 (0.20), residues: 721 sheet: 0.43 (0.17), residues: 854 loop : -1.33 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 44 TYR 0.017 0.002 TYR C1155 PHE 0.020 0.002 PHE A 135 TRP 0.034 0.002 TRP A 152 HIS 0.017 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00366 (29348) covalent geometry : angle 0.57309 (39919) SS BOND : bond 0.00701 ( 39) SS BOND : angle 2.28684 ( 78) hydrogen bonds : bond 0.04349 ( 1002) hydrogen bonds : angle 5.35542 ( 2838) *********************** 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 410 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 289 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.1995 (OUTLIER) cc_final: 0.1793 (tp) REVERT: A 286 THR cc_start: 0.6596 (p) cc_final: 0.6393 (p) REVERT: A 541 PHE cc_start: 0.7342 (p90) cc_final: 0.6936 (p90) REVERT: A 608 VAL cc_start: 0.8234 (t) cc_final: 0.7926 (p) REVERT: A 900 MET cc_start: 0.7830 (mpp) cc_final: 0.7626 (mtp) REVERT: a 83 PHE cc_start: 0.0094 (OUTLIER) cc_final: -0.0188 (m-10) REVERT: a 139 MET cc_start: 0.2053 (ppp) cc_final: 0.0713 (mpp) REVERT: B 153 MET cc_start: 0.0864 (pmm) cc_final: 0.0423 (pmm) REVERT: B 158 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.6504 (mtp85) REVERT: B 559 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.4864 (m-80) REVERT: B 904 TYR cc_start: 0.6782 (t80) cc_final: 0.6558 (t80) REVERT: B 934 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8852 (tt) REVERT: B 1146 ASP cc_start: 0.6487 (m-30) cc_final: 0.6254 (m-30) REVERT: C 200 TYR cc_start: 0.7654 (m-80) cc_final: 0.7219 (m-80) REVERT: C 878 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8083 (tp) REVERT: C 974 SER cc_start: 0.8702 (t) cc_final: 0.8327 (p) outliers start: 121 outliers final: 74 residues processed: 386 average time/residue: 0.1520 time to fit residues: 100.7441 Evaluate side-chains 312 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 232 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 ILE 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 307 THR Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1029 MET 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 197 VAL 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 28 SER Chi-restraints excluded: chain b residue 93 TYR Chi-restraints excluded: chain b residue 137 VAL 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 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 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 559 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 645 THR 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 767 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 986 PRO 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 B residue 1133 VAL 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 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 709 ASN Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 227 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 327 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 284 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 245 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 784 GLN A 856 ASN A 872 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** a 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 762 GLN C 23 GLN C 185 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 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 969 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.169576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.132293 restraints weight = 77247.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.133724 restraints weight = 38158.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.134514 restraints weight = 26143.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.135166 restraints weight = 18570.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.135320 restraints weight = 15775.921| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29387 Z= 0.166 Angle : 0.589 12.744 39997 Z= 0.312 Chirality : 0.045 0.189 4506 Planarity : 0.004 0.061 5163 Dihedral : 4.690 40.297 3924 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.11 % Allowed : 17.04 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3620 helix: 1.06 (0.20), residues: 734 sheet: 0.38 (0.17), residues: 867 loop : -1.27 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 319 TYR 0.024 0.002 TYR A 380 PHE 0.023 0.002 PHE B 168 TRP 0.035 0.002 TRP B 886 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00378 (29348) covalent geometry : angle 0.57889 (39919) SS BOND : bond 0.00830 ( 39) SS BOND : angle 2.54680 ( 78) hydrogen bonds : bond 0.04377 ( 1002) hydrogen bonds : angle 5.23943 ( 2838) *********************** 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 396 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 264 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7138 (m-10) cc_final: 0.6893 (m-80) REVERT: A 286 THR cc_start: 0.6518 (p) cc_final: 0.6297 (p) REVERT: A 541 PHE cc_start: 0.7525 (p90) cc_final: 0.7176 (p90) REVERT: A 608 VAL cc_start: 0.8334 (t) cc_final: 0.8021 (p) REVERT: A 661 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7114 (tm-30) REVERT: a 139 MET cc_start: 0.2067 (ppp) cc_final: 0.0872 (mpp) REVERT: B 102 ARG cc_start: 0.3100 (OUTLIER) cc_final: 0.0725 (mpt180) REVERT: B 153 MET cc_start: 0.1147 (pmm) cc_final: 0.0755 (pmm) REVERT: B 158 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6590 (mtp85) REVERT: B 238 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.5716 (p90) REVERT: B 559 PHE cc_start: 0.5980 (OUTLIER) cc_final: 0.4427 (m-80) REVERT: B 934 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8887 (tt) REVERT: B 1146 ASP cc_start: 0.6466 (m-30) cc_final: 0.6249 (m-30) REVERT: C 200 TYR cc_start: 0.7665 (m-80) cc_final: 0.7385 (m-80) REVERT: C 488 CYS cc_start: 0.2461 (OUTLIER) cc_final: 0.1990 (t) REVERT: C 878 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8062 (tp) REVERT: C 938 LEU cc_start: 0.8420 (mt) cc_final: 0.8213 (mt) REVERT: C 974 SER cc_start: 0.8692 (t) cc_final: 0.8159 (p) outliers start: 132 outliers final: 85 residues processed: 376 average time/residue: 0.1525 time to fit residues: 97.4757 Evaluate side-chains 327 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 235 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 51 THR 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 533 LEU Chi-restraints excluded: chain A residue 747 THR 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 1148 PHE Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 197 VAL 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 137 VAL 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 233 ILE Chi-restraints excluded: chain B residue 238 PHE 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 370 ASN 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 559 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 934 ILE 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 1123 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 42 VAL 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 488 CYS 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 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 768 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 313 optimal weight: 0.0980 chunk 263 optimal weight: 4.9990 chunk 341 optimal weight: 5.9990 chunk 323 optimal weight: 0.7980 chunk 247 optimal weight: 0.6980 chunk 324 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 120 optimal weight: 0.0060 chunk 296 optimal weight: 8.9990 chunk 331 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 856 ASN A 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 171 GLN B 563 GLN B 755 GLN B 935 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 506 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN C1002 GLN C1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.171607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.136704 restraints weight = 77475.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.136909 restraints weight = 41166.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.136920 restraints weight = 31459.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.137667 restraints weight = 25908.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.137705 restraints weight = 22527.955| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 29387 Z= 0.109 Angle : 0.549 12.380 39997 Z= 0.286 Chirality : 0.043 0.216 4506 Planarity : 0.004 0.063 5163 Dihedral : 4.479 39.256 3924 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.11 % Allowed : 18.97 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3620 helix: 1.41 (0.20), residues: 727 sheet: 0.50 (0.17), residues: 859 loop : -1.16 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 319 TYR 0.016 0.001 TYR A 265 PHE 0.021 0.001 PHE A 135 TRP 0.031 0.001 TRP B 886 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00244 (29348) covalent geometry : angle 0.53719 (39919) SS BOND : bond 0.00386 ( 39) SS BOND : angle 2.59603 ( 78) hydrogen bonds : bond 0.03786 ( 1002) hydrogen bonds : angle 4.98374 ( 2838) *********************** 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 366 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 266 time to evaluate : 1.002 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 106 PHE cc_start: 0.7184 (m-10) cc_final: 0.6954 (m-80) REVERT: A 286 THR cc_start: 0.6560 (p) cc_final: 0.6354 (p) REVERT: A 541 PHE cc_start: 0.7545 (p90) cc_final: 0.7245 (p90) REVERT: A 608 VAL cc_start: 0.8147 (t) cc_final: 0.7850 (p) REVERT: a 139 MET cc_start: 0.1972 (ppp) cc_final: 0.0761 (mpp) REVERT: B 102 ARG cc_start: 0.2776 (OUTLIER) cc_final: 0.0628 (mpt180) REVERT: B 153 MET cc_start: 0.1062 (pmm) cc_final: 0.0707 (pmm) REVERT: B 158 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6775 (mtp85) REVERT: B 238 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.5809 (p90) REVERT: B 612 TYR cc_start: 0.8339 (m-80) cc_final: 0.8076 (m-10) REVERT: B 934 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8728 (tt) REVERT: B 1146 ASP cc_start: 0.6570 (m-30) cc_final: 0.6316 (m-30) REVERT: C 200 TYR cc_start: 0.7663 (m-80) cc_final: 0.7450 (m-80) REVERT: C 488 CYS cc_start: 0.2290 (OUTLIER) cc_final: 0.1964 (t) REVERT: C 938 LEU cc_start: 0.8471 (mt) cc_final: 0.8270 (mt) REVERT: C 974 SER cc_start: 0.8466 (t) cc_final: 0.8054 (p) outliers start: 100 outliers final: 68 residues processed: 342 average time/residue: 0.1563 time to fit residues: 90.5662 Evaluate side-chains 317 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 244 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL 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 196 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 331 ASN 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 896 ILE 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 1148 PHE Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 197 VAL 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 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 208 THR Chi-restraints excluded: chain B residue 238 PHE 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 563 GLN 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 754 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 934 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 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 488 CYS Chi-restraints excluded: chain C residue 546 LEU 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 736 VAL Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 59 optimal weight: 0.0020 chunk 227 optimal weight: 0.1980 chunk 192 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 346 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 265 optimal weight: 8.9990 chunk 279 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 920 GLN A 955 ASN ** A1005 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 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.168601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.133801 restraints weight = 77233.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.134537 restraints weight = 44365.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.133874 restraints weight = 31783.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.134268 restraints weight = 28442.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.134379 restraints weight = 25075.041| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.6204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29387 Z= 0.158 Angle : 0.581 9.783 39997 Z= 0.305 Chirality : 0.044 0.182 4506 Planarity : 0.004 0.076 5163 Dihedral : 4.610 39.440 3924 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.52 % Allowed : 19.28 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3620 helix: 1.34 (0.20), residues: 732 sheet: 0.45 (0.17), residues: 869 loop : -1.17 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 319 TYR 0.019 0.002 TYR C 421 PHE 0.032 0.002 PHE B 643 TRP 0.024 0.002 TRP B 886 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00364 (29348) covalent geometry : angle 0.57220 (39919) SS BOND : bond 0.00414 ( 39) SS BOND : angle 2.38780 ( 78) hydrogen bonds : bond 0.04164 ( 1002) hydrogen bonds : angle 5.05205 ( 2838) *********************** 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 378 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 265 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7206 (m-10) cc_final: 0.6867 (m-80) REVERT: A 286 THR cc_start: 0.6570 (p) cc_final: 0.6354 (p) REVERT: A 608 VAL cc_start: 0.8262 (t) cc_final: 0.7967 (p) REVERT: A 661 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7131 (tm-30) REVERT: a 139 MET cc_start: 0.1525 (ppp) cc_final: 0.0532 (mpp) REVERT: a 179 TYR cc_start: 0.4121 (OUTLIER) cc_final: 0.3773 (t80) REVERT: B 87 ASN cc_start: 0.6909 (OUTLIER) cc_final: 0.6348 (p0) REVERT: B 102 ARG cc_start: 0.3086 (OUTLIER) cc_final: 0.0896 (mpt180) REVERT: B 153 MET cc_start: 0.1500 (pmm) cc_final: 0.1256 (pmm) REVERT: B 158 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6499 (mtp85) REVERT: B 238 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.5689 (p90) REVERT: B 317 ASN cc_start: 0.8365 (m-40) cc_final: 0.7955 (m-40) REVERT: B 523 THR cc_start: 0.7546 (OUTLIER) cc_final: 0.7298 (p) REVERT: B 612 TYR cc_start: 0.8432 (m-80) cc_final: 0.8163 (m-10) REVERT: B 934 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8831 (tt) REVERT: B 955 ASN cc_start: 0.8259 (t0) cc_final: 0.8057 (t0) REVERT: C 938 LEU cc_start: 0.8569 (mt) cc_final: 0.8369 (mt) REVERT: C 974 SER cc_start: 0.8542 (t) cc_final: 0.8201 (p) outliers start: 113 outliers final: 80 residues processed: 361 average time/residue: 0.1560 time to fit residues: 95.2640 Evaluate side-chains 328 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 241 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 135 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 351 TYR 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 759 PHE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1001 LEU 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 1148 PHE Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 136 THR Chi-restraints excluded: chain a residue 141 THR Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain a residue 197 VAL 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 87 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE 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 649 CYS 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 767 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 934 ILE 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 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 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 164 optimal weight: 0.7980 chunk 358 optimal weight: 0.9980 chunk 348 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 304 optimal weight: 0.2980 chunk 197 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 6 GLN ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B1159 HIS ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.168801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.134709 restraints weight = 77393.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.134830 restraints weight = 45252.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.134997 restraints weight = 30037.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.135149 restraints weight = 27935.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.135385 restraints weight = 25394.044| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29387 Z= 0.137 Angle : 0.565 9.489 39997 Z= 0.296 Chirality : 0.044 0.216 4506 Planarity : 0.004 0.083 5163 Dihedral : 4.560 38.625 3924 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.18 % Allowed : 19.74 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3620 helix: 1.49 (0.20), residues: 718 sheet: 0.47 (0.17), residues: 873 loop : -1.12 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 319 TYR 0.017 0.001 TYR C 421 PHE 0.047 0.001 PHE A 643 TRP 0.024 0.002 TRP B 886 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00313 (29348) covalent geometry : angle 0.55682 (39919) SS BOND : bond 0.00411 ( 39) SS BOND : angle 2.18208 ( 78) hydrogen bonds : bond 0.04035 ( 1002) hydrogen bonds : angle 4.99707 ( 2838) *********************** 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 361 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 259 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.6649 (m-10) cc_final: 0.6425 (m-80) REVERT: A 286 THR cc_start: 0.6438 (p) cc_final: 0.6118 (p) REVERT: A 608 VAL cc_start: 0.8047 (t) cc_final: 0.7760 (p) REVERT: A 739 THR cc_start: 0.8948 (m) cc_final: 0.8671 (p) REVERT: a 139 MET cc_start: 0.0955 (ppp) cc_final: 0.0181 (mpp) REVERT: a 179 TYR cc_start: 0.4581 (OUTLIER) cc_final: 0.4020 (t80) REVERT: B 102 ARG cc_start: 0.3762 (OUTLIER) cc_final: 0.1260 (mpt180) REVERT: B 203 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7553 (mp) REVERT: B 238 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.5578 (p90) REVERT: B 317 ASN cc_start: 0.8204 (m-40) cc_final: 0.7701 (m-40) REVERT: B 377 PHE cc_start: 0.2241 (OUTLIER) cc_final: 0.1758 (m-80) REVERT: B 559 PHE cc_start: 0.6149 (OUTLIER) cc_final: 0.4465 (m-80) REVERT: B 612 TYR cc_start: 0.8303 (m-80) cc_final: 0.8069 (m-10) REVERT: B 934 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8746 (tt) REVERT: C 488 CYS cc_start: 0.1575 (OUTLIER) cc_final: 0.1338 (t) REVERT: C 938 LEU cc_start: 0.8450 (mt) cc_final: 0.8236 (mt) REVERT: C 974 SER cc_start: 0.8492 (t) cc_final: 0.8253 (p) outliers start: 102 outliers final: 79 residues processed: 342 average time/residue: 0.1592 time to fit residues: 92.2835 Evaluate side-chains 329 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 242 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 135 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 562 PHE 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 872 GLN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1001 LEU 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 1148 PHE Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 136 THR Chi-restraints excluded: chain a residue 141 THR 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 197 VAL 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 119 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE 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 377 PHE 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 559 PHE Chi-restraints excluded: chain B residue 649 CYS 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 767 LEU Chi-restraints excluded: chain B residue 770 ILE 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 934 ILE 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 54 LEU Chi-restraints excluded: chain C residue 66 HIS 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 488 CYS 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 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 126 optimal weight: 5.9990 chunk 315 optimal weight: 8.9990 chunk 129 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 238 optimal weight: 0.9990 chunk 203 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 226 optimal weight: 0.0000 chunk 283 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 175 optimal weight: 0.5980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 955 ASN ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 43 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.170374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.135830 restraints weight = 77355.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.136704 restraints weight = 43640.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.136291 restraints weight = 29421.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.136683 restraints weight = 27902.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.136878 restraints weight = 24549.452| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.6470 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= 0.109 Angle : 0.549 10.996 39997 Z= 0.285 Chirality : 0.043 0.178 4506 Planarity : 0.004 0.080 5163 Dihedral : 4.421 37.871 3924 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.43 % Allowed : 20.55 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3620 helix: 1.54 (0.20), residues: 732 sheet: 0.55 (0.17), residues: 859 loop : -1.09 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1014 TYR 0.015 0.001 TYR C 421 PHE 0.033 0.001 PHE A 643 TRP 0.022 0.001 TRP A 152 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00244 (29348) covalent geometry : angle 0.54290 (39919) SS BOND : bond 0.00431 ( 39) SS BOND : angle 1.98796 ( 78) hydrogen bonds : bond 0.03766 ( 1002) hydrogen bonds : angle 4.90556 ( 2838) *********************** 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 340 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 262 time to evaluate : 1.127 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 106 PHE cc_start: 0.7087 (m-10) cc_final: 0.6745 (m-80) REVERT: A 286 THR cc_start: 0.6420 (p) cc_final: 0.6196 (p) REVERT: A 541 PHE cc_start: 0.7524 (p90) cc_final: 0.7141 (p90) REVERT: A 608 VAL cc_start: 0.8206 (t) cc_final: 0.7915 (p) REVERT: A 823 PHE cc_start: 0.8074 (t80) cc_final: 0.7737 (m-80) REVERT: a 139 MET cc_start: 0.1016 (ppp) cc_final: 0.0177 (mpp) REVERT: a 179 TYR cc_start: 0.4220 (OUTLIER) cc_final: 0.3789 (t80) REVERT: b 6 GLN cc_start: 0.2331 (mt0) cc_final: 0.1131 (mm-40) REVERT: B 102 ARG cc_start: 0.3073 (OUTLIER) cc_final: 0.0816 (mpt180) REVERT: B 238 PHE cc_start: 0.6721 (OUTLIER) cc_final: 0.5739 (p90) REVERT: B 317 ASN cc_start: 0.8365 (m-40) cc_final: 0.7965 (t0) REVERT: B 377 PHE cc_start: 0.2127 (OUTLIER) cc_final: 0.1719 (m-80) REVERT: B 612 TYR cc_start: 0.8454 (m-80) cc_final: 0.8119 (m-10) REVERT: B 934 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8681 (tt) REVERT: C 102 ARG cc_start: 0.1051 (ptt180) cc_final: 0.0786 (ptt180) REVERT: C 974 SER cc_start: 0.8597 (t) cc_final: 0.8268 (p) outliers start: 78 outliers final: 62 residues processed: 324 average time/residue: 0.1592 time to fit residues: 86.8414 Evaluate side-chains 310 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 243 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER 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 196 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR 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 1148 PHE Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 136 THR Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain a residue 197 VAL 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 119 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 238 PHE 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 377 PHE 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 709 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS 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 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 553 THR 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 749 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 1040 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 93 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 153 optimal weight: 0.4980 chunk 131 optimal weight: 8.9990 chunk 311 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 247 optimal weight: 0.6980 chunk 180 optimal weight: 0.8980 chunk 58 optimal weight: 0.0870 chunk 307 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 43 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.171121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.136636 restraints weight = 76952.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.137650 restraints weight = 41304.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.137429 restraints weight = 26713.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.137778 restraints weight = 24879.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.137911 restraints weight = 22822.205| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 29387 Z= 0.103 Angle : 0.542 11.437 39997 Z= 0.281 Chirality : 0.043 0.165 4506 Planarity : 0.004 0.079 5163 Dihedral : 4.290 37.282 3924 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.09 % Allowed : 21.05 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3620 helix: 1.67 (0.20), residues: 732 sheet: 0.59 (0.17), residues: 861 loop : -1.04 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1014 TYR 0.014 0.001 TYR C1067 PHE 0.030 0.001 PHE A 643 TRP 0.021 0.001 TRP A 152 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00230 (29348) covalent geometry : angle 0.53731 (39919) SS BOND : bond 0.00536 ( 39) SS BOND : angle 1.71228 ( 78) hydrogen bonds : bond 0.03542 ( 1002) hydrogen bonds : angle 4.81615 ( 2838) ********************** 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 317 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 250 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7162 (m-10) cc_final: 0.6798 (m-80) REVERT: A 541 PHE cc_start: 0.7441 (p90) cc_final: 0.7065 (p90) REVERT: A 608 VAL cc_start: 0.8107 (t) cc_final: 0.7828 (p) REVERT: A 823 PHE cc_start: 0.8076 (t80) cc_final: 0.7778 (m-80) REVERT: A 955 ASN cc_start: 0.8221 (m-40) cc_final: 0.7758 (t0) REVERT: a 139 MET cc_start: 0.1062 (ppp) cc_final: 0.0208 (mpp) REVERT: a 179 TYR cc_start: 0.4107 (OUTLIER) cc_final: 0.3675 (t80) REVERT: B 87 ASN cc_start: 0.6663 (OUTLIER) cc_final: 0.6450 (p0) REVERT: B 102 ARG cc_start: 0.2981 (OUTLIER) cc_final: 0.0734 (mpt180) REVERT: B 238 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.5678 (p90) REVERT: B 317 ASN cc_start: 0.8221 (m-40) cc_final: 0.7829 (m-40) REVERT: B 377 PHE cc_start: 0.2146 (OUTLIER) cc_final: 0.1771 (m-80) REVERT: B 612 TYR cc_start: 0.8479 (m-80) cc_final: 0.8063 (m-10) REVERT: B 934 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8656 (tt) REVERT: C 974 SER cc_start: 0.8667 (t) cc_final: 0.8303 (p) outliers start: 67 outliers final: 55 residues processed: 304 average time/residue: 0.1571 time to fit residues: 82.0272 Evaluate side-chains 295 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 234 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1148 PHE 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 197 VAL Chi-restraints excluded: chain a residue 210 VAL 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 87 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 238 PHE 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 377 PHE 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 709 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1055 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 238 PHE Chi-restraints excluded: chain C residue 534 VAL 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 736 VAL Chi-restraints excluded: chain C residue 749 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 1040 VAL Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 195 optimal weight: 0.3980 chunk 199 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 174 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 338 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 313 optimal weight: 4.9990 chunk 327 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 190 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 804 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.169107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.135073 restraints weight = 77197.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.134974 restraints weight = 42685.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.135477 restraints weight = 29054.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.135943 restraints weight = 24672.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.136005 restraints weight = 22618.984| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.6704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29387 Z= 0.127 Angle : 0.559 11.746 39997 Z= 0.289 Chirality : 0.044 0.167 4506 Planarity : 0.004 0.077 5163 Dihedral : 4.357 37.476 3924 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.27 % Allowed : 20.80 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3620 helix: 1.65 (0.20), residues: 732 sheet: 0.60 (0.17), residues: 812 loop : -1.08 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1014 TYR 0.014 0.001 TYR C1067 PHE 0.026 0.001 PHE A 643 TRP 0.021 0.002 TRP B 886 HIS 0.008 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00293 (29348) covalent geometry : angle 0.55489 (39919) SS BOND : bond 0.00355 ( 39) SS BOND : angle 1.71115 ( 78) hydrogen bonds : bond 0.03779 ( 1002) hydrogen bonds : angle 4.85799 ( 2838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5396.71 seconds wall clock time: 93 minutes 42.33 seconds (5622.33 seconds total)