Starting phenix.real_space_refine on Sun Sep 13 18:48:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wlz_32595/09_2026/7wlz_32595.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wlz_32595/09_2026/7wlz_32595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wlz_32595/09_2026/7wlz_32595.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wlz_32595/09_2026/7wlz_32595.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wlz_32595/09_2026/7wlz_32595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wlz_32595/09_2026/7wlz_32595.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wlz_32595/09_2026/7wlz_32595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wlz_32595/09_2026/7wlz_32595.map" } resolution = 2.98 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= -0.001 sd= 0.024 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 111 5.16 5 C 16003 2.51 5 N 4132 2.21 5 O 4815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25061 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8046 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 8 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8144 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 56, 'TRANS': 985} Chain breaks: 8 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 6692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 863, 6692 Classifications: {'peptide': 863} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 44, 'TRANS': 818} Chain breaks: 8 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "P" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 1 Chain: "O" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 834 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.46, per 1000 atoms: 0.18 Number of scatterers: 25061 At special positions: 0 Unit cell: (135.876, 137.904, 203.814, 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 111 16.00 O 4815 8.00 N 4132 7.00 C 16003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.01 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.07 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 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 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 93 " distance=2.04 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A1098 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B 331 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 896.1 milliseconds 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5942 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 51 sheets defined 24.6% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.962A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.867A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.894A pdb=" N SER A 637 " --> pdb=" O TRP A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.666A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.592A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 removed outlier: 3.623A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.511A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) 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 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: 3.818A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.608A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.574A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.911A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.681A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.994A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 633 through 638 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 4.009A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.623A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.568A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 915 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.631A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.584A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.543A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.527A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.994A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 857 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.036A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1034 removed outlier: 3.510A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'P' and resid 28 through 32 removed outlier: 4.114A pdb=" N TYR P 32 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 removed outlier: 3.813A pdb=" N THR P 91 " --> pdb=" O ALA P 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.552A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.635A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.537A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.791A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.516A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.731A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.982A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.837A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.169A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.840A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.901A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.304A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB7, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.609A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.097A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP C 586 " --> pdb=" O THR C 553 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.481A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 168 through 172 removed outlier: 3.704A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.585A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.020A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.960A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.625A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.635A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 713 removed outlier: 3.617A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 722 removed outlier: 6.751A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.359A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD6, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AD7, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.584A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.792A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 52 through 55 removed outlier: 4.369A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.556A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.574A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 194 through 197 removed outlier: 5.096A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.533A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.961A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.146A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.466A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF1, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF3, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.664A pdb=" N THR P 124 " --> pdb=" O TYR P 94 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR P 94 " --> pdb=" O THR P 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL P 126 " --> pdb=" O ALA P 92 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 5 through 7 Processing sheet with id=AF6, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.560A pdb=" N LEU O 11 " --> pdb=" O LYS O 108 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP O 110 " --> pdb=" O LEU O 11 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP O 40 " --> pdb=" O LEU O 52 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2508 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.48 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4613 1.33 - 1.45: 7067 1.45 - 1.58: 13804 1.58 - 1.71: 0 1.71 - 1.84: 143 Bond restraints: 25627 Sorted by residual: bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" N ASP C 294 " pdb=" CA ASP C 294 " ideal model delta sigma weight residual 1.456 1.489 -0.032 9.40e-03 1.13e+04 1.16e+01 bond pdb=" N VAL O 88 " pdb=" CA VAL O 88 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.14e-02 7.69e+03 1.16e+01 bond pdb=" N ILE B 472 " pdb=" CA ILE B 472 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.15e+01 bond pdb=" N LEU B 492 " pdb=" CA LEU B 492 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.18e-02 7.18e+03 1.13e+01 ... (remaining 25622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 33895 2.50 - 4.99: 889 4.99 - 7.49: 67 7.49 - 9.99: 10 9.99 - 12.49: 3 Bond angle restraints: 34864 Sorted by residual: angle pdb=" N LEU B 368 " pdb=" CA LEU B 368 " pdb=" C LEU B 368 " ideal model delta sigma weight residual 113.41 101.76 11.65 1.22e+00 6.72e-01 9.12e+01 angle pdb=" N GLY B 404 " pdb=" CA GLY B 404 " pdb=" C GLY B 404 " ideal model delta sigma weight residual 112.49 121.41 -8.92 1.21e+00 6.83e-01 5.44e+01 angle pdb=" C VAL B 367 " pdb=" CA VAL B 367 " pdb=" CB VAL B 367 " ideal model delta sigma weight residual 112.14 103.43 8.71 1.35e+00 5.49e-01 4.16e+01 angle pdb=" N VAL B 367 " pdb=" CA VAL B 367 " pdb=" C VAL B 367 " ideal model delta sigma weight residual 110.62 116.55 -5.93 1.02e+00 9.61e-01 3.38e+01 angle pdb=" CA ILE B 410 " pdb=" C ILE B 410 " pdb=" O ILE B 410 " ideal model delta sigma weight residual 122.63 117.93 4.70 8.70e-01 1.32e+00 2.92e+01 ... (remaining 34859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 13793 17.75 - 35.50: 1062 35.50 - 53.25: 155 53.25 - 71.00: 36 71.00 - 88.75: 22 Dihedral angle restraints: 15068 sinusoidal: 5848 harmonic: 9220 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -178.66 -88.34 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -171.58 85.58 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -171.09 85.09 1 1.00e+01 1.00e-02 8.78e+01 ... (remaining 15065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 3977 0.160 - 0.319: 63 0.319 - 0.479: 4 0.479 - 0.639: 0 0.639 - 0.798: 1 Chirality restraints: 4045 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 4042 not shown) Planarity restraints: 4495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " -0.339 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG B1308 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " -0.085 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1306 " -0.333 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG B1306 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B1306 " -0.142 2.00e-02 2.50e+03 pdb=" N2 NAG B1306 " 0.514 2.00e-02 2.50e+03 pdb=" O7 NAG B1306 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " 0.331 2.00e-02 2.50e+03 2.82e-01 9.97e+02 pdb=" C7 NAG A1301 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " -0.497 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.077 2.00e-02 2.50e+03 ... (remaining 4492 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2942 2.75 - 3.29: 25168 3.29 - 3.82: 39860 3.82 - 4.36: 47193 4.36 - 4.90: 83220 Nonbonded interactions: 198383 Sorted by model distance: nonbonded pdb=" O TRP B 633 " pdb=" OG SER B 637 " model vdw 2.212 3.040 nonbonded pdb=" O THR C 747 " pdb=" OG SER C 750 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLU B 819 " pdb=" OG SER B1055 " model vdw 2.240 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.265 3.040 ... (remaining 198378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O or name CB )) or resid 103 through 118 or (resid 119 and (name N o \ r name CA or name C or name O or name CB )) or resid 120 through 209 or (resid 2 \ 10 and (name N or name CA or name C or name O or name CB )) or resid 212 through \ 228 or (resid 229 and (name N or name CA or name C or name O or name CB )) or r \ esid 230 or (resid 231 and (name N or name CA or name C or name O or name CB )) \ or resid 232 through 333 or (resid 334 and (name N or name CA or name C or name \ O or name CB )) or resid 335 through 461 or (resid 462 and (name N or name CA or \ name C or name O or name CB )) or resid 463 through 502 or (resid 503 and (name \ N or name CA or name C or name O or name CB )) or resid 504 through 556 or (res \ id 557 through 558 and (name N or name CA or name C or name O or name CB )) or r \ esid 559 through 622 or resid 632 through 1309)) selection = (chain 'B' and (resid 27 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 429 or (resid 430 and (name N o \ r name CA or name C or name O or name CB )) or resid 431 through 468 or resid 49 \ 2 through 536 or (resid 537 and (name N or name CA or name C or name O or name C \ B )) or resid 538 through 562 or (resid 563 and (name N or name CA or name C or \ name O or name CB )) or resid 564 through 579 or (resid 580 and (name N or name \ CA or name C or name O or name CB )) or resid 581 through 1309)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 22.160 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.006 0.078 25690 Z= 0.369 Angle : 0.910 12.485 35017 Z= 0.573 Chirality : 0.059 0.798 4045 Planarity : 0.012 0.294 4468 Dihedral : 12.885 88.752 9018 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.15 % Allowed : 1.83 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.14), residues: 3111 helix: 0.42 (0.20), residues: 688 sheet: -1.78 (0.18), residues: 745 loop : -2.30 (0.13), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 273 TYR 0.016 0.001 TYR B1067 PHE 0.031 0.002 PHE A 906 TRP 0.027 0.002 TRP C 633 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.37 (25627) covalent geometry : angle 0.89867 / 0.57 (34864) SS BOND : bond 0.00938 / 0.49 ( 36) SS BOND : angle 2.03004 / 1.35 ( 72) hydrogen bonds : bond 0.20537 / 13.33 ( 920) hydrogen bonds : angle 8.82159 / 5.97 ( 2508) link_NAG-ASN : bond 0.00645 / 0.43 ( 27) link_NAG-ASN : angle 2.63910 / 1.75 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 243 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 577 ARG cc_start: 0.6871 (ttp-170) cc_final: 0.6646 (ttm-80) REVERT: A 886 TRP cc_start: 0.8100 (p90) cc_final: 0.7548 (p90) REVERT: B 88 ASP cc_start: 0.7513 (m-30) cc_final: 0.7053 (p0) REVERT: B 226 LEU cc_start: 0.8265 (tp) cc_final: 0.8019 (pp) REVERT: B 544 ASN cc_start: 0.6982 (m-40) cc_final: 0.6701 (m-40) REVERT: B 1010 GLN cc_start: 0.7916 (mp10) cc_final: 0.7493 (mp10) REVERT: C 44 ARG cc_start: 0.7645 (mtt90) cc_final: 0.7404 (mtt90) REVERT: P 102 MET cc_start: 0.6143 (mtm) cc_final: 0.5934 (mpm) REVERT: O 7 SER cc_start: 0.6280 (m) cc_final: 0.6015 (p) outliers start: 4 outliers final: 0 residues processed: 246 average time/residue: 0.5742 time to fit residues: 165.9754 Evaluate side-chains 155 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 134 GLN A 164 ASN A 314 GLN A 370 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 542 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 901 GLN A 919 ASN A1002 GLN A1119 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 317 ASN B 448 ASN B 450 ASN B 564 GLN B 606 ASN B 804 GLN B 957 GLN B 960 ASN C 121 ASN C 271 GLN C 280 ASN C 317 ASN C 625 HIS C 644 GLN C 751 ASN C 901 GLN C 935 GLN C 965 GLN C1002 GLN P 39 GLN O 31 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.170902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.103720 restraints weight = 46647.998| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.82 r_work: 0.3235 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 25690 Z= 0.242 Angle : 0.735 13.637 35017 Z= 0.368 Chirality : 0.050 0.325 4045 Planarity : 0.005 0.077 4468 Dihedral : 5.028 40.113 3387 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.75 % Allowed : 9.24 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.83 (0.14), residues: 3111 helix: 0.94 (0.19), residues: 694 sheet: -1.45 (0.18), residues: 776 loop : -2.11 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 983 TYR 0.027 0.002 TYR C1067 PHE 0.028 0.002 PHE B 906 TRP 0.021 0.002 TRP C 633 HIS 0.007 0.001 HIS P 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.24 (25627) covalent geometry : angle 0.72067 / 0.36 (34864) SS BOND : bond 0.00462 / 0.28 ( 36) SS BOND : angle 1.77470 / 1.25 ( 72) hydrogen bonds : bond 0.05765 / 3.83 ( 920) hydrogen bonds : angle 6.46013 / 4.37 ( 2508) link_NAG-ASN : bond 0.00550 / 0.39 ( 27) link_NAG-ASN : angle 2.70066 / 1.80 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7919 (m-80) cc_final: 0.7626 (m-80) REVERT: A 200 TYR cc_start: 0.8777 (m-80) cc_final: 0.8562 (m-80) REVERT: A 542 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.6983 (t0) REVERT: A 577 ARG cc_start: 0.7063 (ttp-170) cc_final: 0.6796 (ttm-80) REVERT: A 974 SER cc_start: 0.8674 (m) cc_final: 0.8384 (p) REVERT: B 88 ASP cc_start: 0.7773 (m-30) cc_final: 0.7235 (p0) REVERT: B 226 LEU cc_start: 0.8292 (tp) cc_final: 0.7884 (pp) REVERT: B 278 LYS cc_start: 0.8556 (tttt) cc_final: 0.8313 (tmmm) REVERT: B 329 PHE cc_start: 0.8048 (t80) cc_final: 0.7725 (t80) REVERT: B 544 ASN cc_start: 0.7113 (m-40) cc_final: 0.6874 (m-40) REVERT: B 979 ASP cc_start: 0.8143 (t0) cc_final: 0.7734 (t0) REVERT: B 983 ARG cc_start: 0.8680 (ttp80) cc_final: 0.7835 (ptt90) REVERT: C 33 THR cc_start: 0.5463 (OUTLIER) cc_final: 0.5034 (p) REVERT: C 65 PHE cc_start: 0.7560 (m-10) cc_final: 0.7236 (m-10) REVERT: C 298 GLU cc_start: 0.7589 (mp0) cc_final: 0.7357 (mp0) REVERT: C 759 PHE cc_start: 0.7618 (m-80) cc_final: 0.7412 (m-80) REVERT: O 4 MET cc_start: 0.4844 (mpp) cc_final: 0.2845 (pmm) outliers start: 48 outliers final: 16 residues processed: 207 average time/residue: 0.4810 time to fit residues: 119.9753 Evaluate side-chains 167 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain O residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 95 optimal weight: 3.9990 chunk 296 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 291 optimal weight: 0.9980 chunk 257 optimal weight: 0.7980 chunk 136 optimal weight: 0.0570 chunk 293 optimal weight: 0.0170 chunk 26 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 307 optimal weight: 20.0000 chunk 37 optimal weight: 30.0000 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 542 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1119 ASN B 49 HIS B 505 HIS B1002 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.172791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.106112 restraints weight = 46560.738| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.93 r_work: 0.3263 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25690 Z= 0.133 Angle : 0.635 10.926 35017 Z= 0.315 Chirality : 0.046 0.290 4045 Planarity : 0.004 0.050 4468 Dihedral : 4.693 37.768 3387 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.86 % Allowed : 11.68 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.45 (0.15), residues: 3111 helix: 1.29 (0.20), residues: 692 sheet: -1.12 (0.19), residues: 759 loop : -1.94 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 273 TYR 0.022 0.001 TYR C1067 PHE 0.024 0.001 PHE C 192 TRP 0.013 0.001 TRP B 886 HIS 0.009 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (25627) covalent geometry : angle 0.62315 / 0.31 (34864) SS BOND : bond 0.00302 / 0.20 ( 36) SS BOND : angle 1.60197 / 1.10 ( 72) hydrogen bonds : bond 0.04690 / 3.10 ( 920) hydrogen bonds : angle 5.95724 / 4.03 ( 2508) link_NAG-ASN : bond 0.00457 / 0.34 ( 27) link_NAG-ASN : angle 2.25073 / 1.49 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7989 (m-80) cc_final: 0.7632 (m-80) REVERT: A 200 TYR cc_start: 0.8794 (m-80) cc_final: 0.8584 (m-80) REVERT: A 577 ARG cc_start: 0.7021 (ttp-170) cc_final: 0.6803 (ttm-80) REVERT: A 886 TRP cc_start: 0.8483 (p90) cc_final: 0.7807 (p90) REVERT: A 974 SER cc_start: 0.8696 (m) cc_final: 0.8440 (p) REVERT: A 976 VAL cc_start: 0.8174 (OUTLIER) cc_final: 0.7745 (m) REVERT: A 1010 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8544 (mp10) REVERT: B 88 ASP cc_start: 0.7636 (m-30) cc_final: 0.7036 (p0) REVERT: B 177 MET cc_start: 0.7565 (pmt) cc_final: 0.6913 (mmt) REVERT: B 278 LYS cc_start: 0.8459 (tttt) cc_final: 0.8196 (tmmm) REVERT: B 329 PHE cc_start: 0.8044 (t80) cc_final: 0.7703 (t80) REVERT: B 979 ASP cc_start: 0.8209 (t0) cc_final: 0.7742 (t0) REVERT: B 983 ARG cc_start: 0.8726 (ttp80) cc_final: 0.7849 (ptt90) REVERT: C 65 PHE cc_start: 0.7305 (m-10) cc_final: 0.6939 (m-10) REVERT: C 762 GLN cc_start: 0.8560 (mp10) cc_final: 0.8023 (mp10) REVERT: C 990 GLU cc_start: 0.8409 (pp20) cc_final: 0.8123 (pp20) REVERT: O 4 MET cc_start: 0.4684 (mpp) cc_final: 0.3067 (pmm) outliers start: 51 outliers final: 26 residues processed: 209 average time/residue: 0.4626 time to fit residues: 116.5097 Evaluate side-chains 177 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 232 optimal weight: 10.0000 chunk 288 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 309 optimal weight: 7.9990 chunk 203 optimal weight: 0.9990 chunk 299 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1119 ASN B1088 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.169521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.101564 restraints weight = 46340.407| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.87 r_work: 0.3210 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 25690 Z= 0.270 Angle : 0.714 10.428 35017 Z= 0.356 Chirality : 0.049 0.326 4045 Planarity : 0.005 0.050 4468 Dihedral : 4.897 37.828 3387 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.88 % Allowed : 13.22 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.52 (0.14), residues: 3111 helix: 1.07 (0.20), residues: 687 sheet: -1.08 (0.18), residues: 778 loop : -1.94 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.025 0.002 TYR C1067 PHE 0.023 0.002 PHE C 192 TRP 0.025 0.002 TRP B 886 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.27 (25627) covalent geometry : angle 0.69684 / 0.35 (34864) SS BOND : bond 0.00562 / 0.36 ( 36) SS BOND : angle 2.27004 / 1.59 ( 72) hydrogen bonds : bond 0.05485 / 3.68 ( 920) hydrogen bonds : angle 5.97012 / 4.05 ( 2508) link_NAG-ASN : bond 0.00549 / 0.40 ( 27) link_NAG-ASN : angle 2.60224 / 1.73 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 161 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8790 (m-80) cc_final: 0.8546 (m-80) REVERT: A 1010 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8672 (mp10) REVERT: B 88 ASP cc_start: 0.7744 (m-30) cc_final: 0.7277 (p0) REVERT: B 177 MET cc_start: 0.7576 (pmt) cc_final: 0.6847 (tpp) REVERT: B 194 PHE cc_start: 0.7952 (m-80) cc_final: 0.7714 (m-10) REVERT: B 329 PHE cc_start: 0.7938 (t80) cc_final: 0.7623 (m-80) REVERT: B 979 ASP cc_start: 0.8262 (t0) cc_final: 0.8054 (t0) REVERT: B 983 ARG cc_start: 0.8784 (ttp80) cc_final: 0.8519 (ttp80) REVERT: C 65 PHE cc_start: 0.7499 (m-10) cc_final: 0.7112 (m-10) REVERT: C 319 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7249 (mmm160) REVERT: C 762 GLN cc_start: 0.8628 (mp10) cc_final: 0.8299 (mp10) REVERT: C 1002 GLN cc_start: 0.8967 (tt0) cc_final: 0.8534 (tp-100) REVERT: P 65 LYS cc_start: 0.1299 (OUTLIER) cc_final: -0.0211 (tttt) REVERT: O 4 MET cc_start: 0.4664 (mpp) cc_final: 0.3099 (pmm) REVERT: O 11 LEU cc_start: 0.3519 (pt) cc_final: 0.3132 (tt) outliers start: 79 outliers final: 41 residues processed: 221 average time/residue: 0.4411 time to fit residues: 118.4838 Evaluate side-chains 188 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain O residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 268 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 206 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 257 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 249 optimal weight: 0.8980 chunk 286 optimal weight: 0.8980 chunk 240 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 755 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 580 GLN P 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.172153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.105544 restraints weight = 46196.323| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.83 r_work: 0.3261 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25690 Z= 0.126 Angle : 0.623 11.887 35017 Z= 0.306 Chirality : 0.045 0.289 4045 Planarity : 0.004 0.046 4468 Dihedral : 4.559 33.983 3387 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.48 % Allowed : 14.49 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.22 (0.15), residues: 3111 helix: 1.43 (0.20), residues: 690 sheet: -0.96 (0.19), residues: 762 loop : -1.76 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 72 TYR 0.020 0.001 TYR C1067 PHE 0.030 0.001 PHE A 133 TRP 0.014 0.001 TRP B 886 HIS 0.020 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (25627) covalent geometry : angle 0.61037 / 0.30 (34864) SS BOND : bond 0.00334 / 0.22 ( 36) SS BOND : angle 1.68763 / 1.16 ( 72) hydrogen bonds : bond 0.04344 / 2.88 ( 920) hydrogen bonds : angle 5.62660 / 3.81 ( 2508) link_NAG-ASN : bond 0.00444 / 0.33 ( 27) link_NAG-ASN : angle 2.17959 / 1.44 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 159 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8767 (m-80) cc_final: 0.8515 (m-80) REVERT: A 886 TRP cc_start: 0.8471 (p90) cc_final: 0.7793 (p90) REVERT: A 1010 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8550 (mp10) REVERT: B 88 ASP cc_start: 0.7645 (m-30) cc_final: 0.7190 (p0) REVERT: B 177 MET cc_start: 0.7638 (pmt) cc_final: 0.6955 (tpp) REVERT: B 191 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7127 (mp0) REVERT: B 329 PHE cc_start: 0.7774 (t80) cc_final: 0.7509 (m-80) REVERT: B 979 ASP cc_start: 0.8321 (t0) cc_final: 0.8085 (t0) REVERT: B 983 ARG cc_start: 0.8780 (ttp80) cc_final: 0.8524 (ttp80) REVERT: C 65 PHE cc_start: 0.7249 (m-10) cc_final: 0.6836 (m-10) REVERT: C 319 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.7131 (mtp-110) REVERT: C 762 GLN cc_start: 0.8626 (mp10) cc_final: 0.8311 (mp10) REVERT: C 990 GLU cc_start: 0.8474 (pp20) cc_final: 0.8127 (pp20) REVERT: C 992 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: P 65 LYS cc_start: 0.1350 (OUTLIER) cc_final: -0.0072 (tttt) REVERT: O 4 MET cc_start: 0.4734 (mpp) cc_final: 0.3083 (pmm) REVERT: O 11 LEU cc_start: 0.3508 (pt) cc_final: 0.3078 (tt) outliers start: 68 outliers final: 30 residues processed: 214 average time/residue: 0.4398 time to fit residues: 115.0687 Evaluate side-chains 183 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 302 optimal weight: 10.0000 chunk 245 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 247 optimal weight: 0.0000 chunk 285 optimal weight: 0.2980 chunk 126 optimal weight: 0.2980 chunk 261 optimal weight: 0.0870 chunk 55 optimal weight: 0.6980 chunk 212 optimal weight: 4.9990 chunk 288 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 overall best weight: 0.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A1002 GLN A1119 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.172178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.105976 restraints weight = 45464.610| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.85 r_work: 0.3297 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25690 Z= 0.106 Angle : 0.597 10.750 35017 Z= 0.291 Chirality : 0.045 0.286 4045 Planarity : 0.004 0.044 4468 Dihedral : 4.341 34.099 3387 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.23 % Allowed : 15.04 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.15), residues: 3111 helix: 1.69 (0.21), residues: 683 sheet: -0.69 (0.19), residues: 748 loop : -1.62 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 577 TYR 0.019 0.001 TYR C1067 PHE 0.028 0.001 PHE A 133 TRP 0.010 0.001 TRP B 886 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (25627) covalent geometry : angle 0.58526 / 0.29 (34864) SS BOND : bond 0.00314 / 0.21 ( 36) SS BOND : angle 1.55223 / 1.20 ( 72) hydrogen bonds : bond 0.03906 / 2.58 ( 920) hydrogen bonds : angle 5.38144 / 3.64 ( 2508) link_NAG-ASN : bond 0.00452 / 0.33 ( 27) link_NAG-ASN : angle 2.08233 / 1.37 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 166 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8819 (m-80) cc_final: 0.8536 (m-80) REVERT: A 886 TRP cc_start: 0.8516 (p90) cc_final: 0.7783 (p90) REVERT: A 1010 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8339 (mp10) REVERT: B 88 ASP cc_start: 0.7722 (m-30) cc_final: 0.7186 (p0) REVERT: B 177 MET cc_start: 0.7641 (pmt) cc_final: 0.6950 (tpt) REVERT: B 191 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7055 (mp0) REVERT: B 329 PHE cc_start: 0.7806 (t80) cc_final: 0.7597 (m-80) REVERT: B 979 ASP cc_start: 0.8262 (t0) cc_final: 0.8012 (t0) REVERT: B 983 ARG cc_start: 0.8841 (ttp80) cc_final: 0.8544 (ttp80) REVERT: C 65 PHE cc_start: 0.7116 (m-10) cc_final: 0.6719 (m-10) REVERT: C 762 GLN cc_start: 0.8610 (mp10) cc_final: 0.8354 (mp10) REVERT: C 776 LYS cc_start: 0.8294 (tmmt) cc_final: 0.8085 (tmmt) REVERT: C 990 GLU cc_start: 0.8479 (pp20) cc_final: 0.8150 (pp20) REVERT: P 65 LYS cc_start: 0.1438 (OUTLIER) cc_final: 0.0033 (tttt) REVERT: O 4 MET cc_start: 0.4578 (mpp) cc_final: 0.3029 (pmm) REVERT: O 11 LEU cc_start: 0.3556 (pt) cc_final: 0.3106 (tt) outliers start: 61 outliers final: 28 residues processed: 215 average time/residue: 0.4754 time to fit residues: 124.4449 Evaluate side-chains 181 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain P residue 65 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 23 optimal weight: 0.7980 chunk 302 optimal weight: 50.0000 chunk 18 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 chunk 129 optimal weight: 30.0000 chunk 59 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 287 optimal weight: 1.9990 chunk 68 optimal weight: 0.0020 chunk 304 optimal weight: 20.0000 chunk 235 optimal weight: 2.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A1002 GLN A1119 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.171449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.104366 restraints weight = 46278.018| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.88 r_work: 0.3249 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25690 Z= 0.161 Angle : 0.638 12.942 35017 Z= 0.311 Chirality : 0.046 0.299 4045 Planarity : 0.004 0.050 4468 Dihedral : 4.404 33.682 3387 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.86 % Allowed : 16.21 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.99 (0.15), residues: 3111 helix: 1.54 (0.20), residues: 692 sheet: -0.76 (0.19), residues: 760 loop : -1.61 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 34 TYR 0.023 0.001 TYR A 904 PHE 0.028 0.001 PHE A 133 TRP 0.014 0.001 TRP B 886 HIS 0.015 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (25627) covalent geometry : angle 0.62459 / 0.31 (34864) SS BOND : bond 0.00380 / 0.25 ( 36) SS BOND : angle 1.93954 / 1.33 ( 72) hydrogen bonds : bond 0.04317 / 2.88 ( 920) hydrogen bonds : angle 5.38914 / 3.65 ( 2508) link_NAG-ASN : bond 0.00437 / 0.33 ( 27) link_NAG-ASN : angle 2.20239 / 1.46 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8811 (m-80) cc_final: 0.8593 (m-80) REVERT: A 1010 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8453 (mp10) REVERT: B 88 ASP cc_start: 0.7689 (m-30) cc_final: 0.7196 (p0) REVERT: B 177 MET cc_start: 0.7700 (pmt) cc_final: 0.6984 (tpt) REVERT: B 191 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7110 (mp0) REVERT: B 983 ARG cc_start: 0.8816 (ttp80) cc_final: 0.8594 (ttp80) REVERT: C 65 PHE cc_start: 0.7323 (m-10) cc_final: 0.6949 (m-10) REVERT: C 193 VAL cc_start: 0.7672 (t) cc_final: 0.7407 (t) REVERT: C 762 GLN cc_start: 0.8624 (mp10) cc_final: 0.8404 (mp10) REVERT: P 65 LYS cc_start: 0.1291 (OUTLIER) cc_final: -0.0260 (tttt) REVERT: O 4 MET cc_start: 0.4653 (mpp) cc_final: 0.3010 (pmm) REVERT: O 11 LEU cc_start: 0.3543 (pt) cc_final: 0.3053 (tt) outliers start: 51 outliers final: 32 residues processed: 196 average time/residue: 0.4586 time to fit residues: 110.3245 Evaluate side-chains 183 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 216 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 196 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 129 optimal weight: 50.0000 chunk 250 optimal weight: 0.6980 chunk 110 optimal weight: 20.0000 chunk 225 optimal weight: 6.9990 chunk 271 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A1002 GLN A1119 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.171038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.104040 restraints weight = 46077.097| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.82 r_work: 0.3216 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25690 Z= 0.174 Angle : 0.642 10.635 35017 Z= 0.315 Chirality : 0.046 0.301 4045 Planarity : 0.004 0.056 4468 Dihedral : 4.425 33.341 3387 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.01 % Allowed : 16.65 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.99 (0.15), residues: 3111 helix: 1.50 (0.20), residues: 692 sheet: -0.72 (0.19), residues: 757 loop : -1.60 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.025 0.001 TYR A 904 PHE 0.028 0.001 PHE A 133 TRP 0.017 0.001 TRP C 104 HIS 0.010 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.17 (25627) covalent geometry : angle 0.62928 / 0.31 (34864) SS BOND : bond 0.00445 / 0.25 ( 36) SS BOND : angle 1.83400 / 1.25 ( 72) hydrogen bonds : bond 0.04465 / 2.98 ( 920) hydrogen bonds : angle 5.40320 / 3.66 ( 2508) link_NAG-ASN : bond 0.00439 / 0.33 ( 27) link_NAG-ASN : angle 2.22367 / 1.48 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 153 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 985 ASP cc_start: 0.7440 (p0) cc_final: 0.6430 (p0) REVERT: A 1010 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8428 (mp10) REVERT: B 88 ASP cc_start: 0.7711 (m-30) cc_final: 0.7168 (p0) REVERT: B 177 MET cc_start: 0.7703 (pmt) cc_final: 0.6989 (tpt) REVERT: B 191 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7041 (mp0) REVERT: B 934 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7941 (mp) REVERT: C 58 PHE cc_start: 0.6894 (OUTLIER) cc_final: 0.6561 (t80) REVERT: C 65 PHE cc_start: 0.7366 (m-10) cc_final: 0.6959 (m-10) REVERT: C 193 VAL cc_start: 0.7634 (t) cc_final: 0.7359 (t) REVERT: C 762 GLN cc_start: 0.8637 (mp10) cc_final: 0.8381 (mp10) REVERT: C 990 GLU cc_start: 0.8443 (pp20) cc_final: 0.8129 (pp20) REVERT: P 65 LYS cc_start: 0.1335 (OUTLIER) cc_final: -0.0037 (tttt) REVERT: O 4 MET cc_start: 0.4546 (mpp) cc_final: 0.2874 (pmm) REVERT: O 11 LEU cc_start: 0.3583 (pt) cc_final: 0.3099 (tt) outliers start: 55 outliers final: 38 residues processed: 198 average time/residue: 0.4351 time to fit residues: 105.8270 Evaluate side-chains 190 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 3 optimal weight: 0.7980 chunk 166 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 249 optimal weight: 0.6980 chunk 118 optimal weight: 0.3980 chunk 29 optimal weight: 30.0000 chunk 273 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 286 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A1002 GLN A1119 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.171278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.104720 restraints weight = 45109.742| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.87 r_work: 0.3276 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25690 Z= 0.115 Angle : 0.624 13.153 35017 Z= 0.302 Chirality : 0.045 0.282 4045 Planarity : 0.004 0.051 4468 Dihedral : 4.313 31.446 3387 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.64 % Allowed : 17.23 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.83 (0.15), residues: 3111 helix: 1.61 (0.20), residues: 692 sheet: -0.61 (0.19), residues: 745 loop : -1.49 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 983 TYR 0.019 0.001 TYR A 904 PHE 0.029 0.001 PHE A 133 TRP 0.021 0.001 TRP C 104 HIS 0.010 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (25627) covalent geometry : angle 0.61352 / 0.30 (34864) SS BOND : bond 0.00298 / 0.20 ( 36) SS BOND : angle 1.55024 / 1.06 ( 72) hydrogen bonds : bond 0.03973 / 2.63 ( 920) hydrogen bonds : angle 5.27100 / 3.57 ( 2508) link_NAG-ASN : bond 0.00437 / 0.32 ( 27) link_NAG-ASN : angle 2.07506 / 1.37 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8801 (m-80) cc_final: 0.8552 (m-80) REVERT: A 886 TRP cc_start: 0.8513 (p90) cc_final: 0.7873 (p90) REVERT: A 912 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8661 (p) REVERT: A 1010 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8370 (mp10) REVERT: B 52 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 88 ASP cc_start: 0.7735 (m-30) cc_final: 0.7254 (p0) REVERT: B 177 MET cc_start: 0.7681 (pmt) cc_final: 0.6971 (tpt) REVERT: B 191 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7037 (mp0) REVERT: B 226 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8200 (pt) REVERT: B 979 ASP cc_start: 0.8064 (t0) cc_final: 0.7571 (t0) REVERT: B 983 ARG cc_start: 0.8631 (ttp80) cc_final: 0.7766 (ptt90) REVERT: C 58 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.6508 (t80) REVERT: C 65 PHE cc_start: 0.7207 (m-10) cc_final: 0.6826 (m-10) REVERT: C 193 VAL cc_start: 0.7557 (t) cc_final: 0.7301 (t) REVERT: C 762 GLN cc_start: 0.8579 (mp10) cc_final: 0.8312 (mp10) REVERT: C 990 GLU cc_start: 0.8482 (pp20) cc_final: 0.8151 (pp20) REVERT: P 34 MET cc_start: 0.3561 (mmt) cc_final: 0.1944 (ptp) REVERT: P 65 LYS cc_start: 0.1440 (OUTLIER) cc_final: 0.0065 (tttt) REVERT: O 4 MET cc_start: 0.4503 (mpp) cc_final: 0.2932 (pmm) REVERT: O 11 LEU cc_start: 0.3642 (pt) cc_final: 0.3171 (tt) REVERT: O 52 LEU cc_start: 0.3803 (tm) cc_final: 0.3410 (tt) outliers start: 45 outliers final: 30 residues processed: 195 average time/residue: 0.4557 time to fit residues: 108.5919 Evaluate side-chains 185 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 200 optimal weight: 0.3980 chunk 43 optimal weight: 20.0000 chunk 65 optimal weight: 0.4980 chunk 312 optimal weight: 30.0000 chunk 199 optimal weight: 0.9990 chunk 229 optimal weight: 0.0060 chunk 175 optimal weight: 0.0270 chunk 127 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A1002 GLN A1005 GLN C 317 ASN C 751 ASN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.172239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.108365 restraints weight = 45366.849| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.26 r_work: 0.3274 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25690 Z= 0.108 Angle : 0.620 20.443 35017 Z= 0.299 Chirality : 0.045 0.286 4045 Planarity : 0.004 0.052 4468 Dihedral : 4.197 30.363 3387 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.57 % Allowed : 17.49 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.73 (0.15), residues: 3111 helix: 1.67 (0.20), residues: 692 sheet: -0.57 (0.19), residues: 756 loop : -1.42 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 983 TYR 0.019 0.001 TYR C1067 PHE 0.035 0.001 PHE C 192 TRP 0.023 0.001 TRP C 104 HIS 0.017 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (25627) covalent geometry : angle 0.61026 / 0.30 (34864) SS BOND : bond 0.00279 / 0.19 ( 36) SS BOND : angle 1.39982 / 0.98 ( 72) hydrogen bonds : bond 0.03749 / 2.47 ( 920) hydrogen bonds : angle 5.16319 / 3.50 ( 2508) link_NAG-ASN : bond 0.00437 / 0.32 ( 27) link_NAG-ASN : angle 2.02843 / 1.34 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8782 (m-80) cc_final: 0.8567 (m-80) REVERT: A 886 TRP cc_start: 0.8440 (p90) cc_final: 0.7744 (p90) REVERT: A 912 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8517 (p) REVERT: A 1010 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8119 (mp10) REVERT: B 52 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7826 (tm-30) REVERT: B 88 ASP cc_start: 0.7588 (m-30) cc_final: 0.7235 (p0) REVERT: B 177 MET cc_start: 0.7670 (pmt) cc_final: 0.6961 (tpt) REVERT: B 191 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7053 (mp0) REVERT: B 226 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8078 (mm) REVERT: B 979 ASP cc_start: 0.7954 (t0) cc_final: 0.7494 (t0) REVERT: B 983 ARG cc_start: 0.8620 (ttp80) cc_final: 0.7918 (ptt90) REVERT: C 58 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.6204 (t80) REVERT: C 65 PHE cc_start: 0.7161 (m-10) cc_final: 0.6756 (m-10) REVERT: C 193 VAL cc_start: 0.7354 (t) cc_final: 0.7107 (t) REVERT: C 646 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8135 (mtp-110) REVERT: C 762 GLN cc_start: 0.8435 (mp10) cc_final: 0.8173 (mp10) REVERT: C 990 GLU cc_start: 0.8392 (pp20) cc_final: 0.8071 (pp20) REVERT: P 34 MET cc_start: 0.3689 (mmt) cc_final: 0.2064 (ptp) REVERT: P 65 LYS cc_start: 0.1650 (OUTLIER) cc_final: 0.0213 (tttt) REVERT: O 4 MET cc_start: 0.4329 (mpp) cc_final: 0.2848 (pmm) REVERT: O 11 LEU cc_start: 0.3752 (pt) cc_final: 0.3305 (tt) REVERT: O 52 LEU cc_start: 0.3895 (tm) cc_final: 0.3624 (tt) outliers start: 43 outliers final: 30 residues processed: 193 average time/residue: 0.4514 time to fit residues: 106.9478 Evaluate side-chains 188 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 246 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 224 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 chunk 10 optimal weight: 0.0670 chunk 105 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A1002 GLN C 317 ASN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.169171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.102695 restraints weight = 45080.735| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.40 r_work: 0.3237 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25690 Z= 0.123 Angle : 0.633 15.130 35017 Z= 0.304 Chirality : 0.045 0.290 4045 Planarity : 0.004 0.043 4468 Dihedral : 4.175 29.385 3387 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.61 % Allowed : 17.63 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.15), residues: 3111 helix: 1.64 (0.20), residues: 695 sheet: -0.52 (0.19), residues: 754 loop : -1.38 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 983 TYR 0.022 0.001 TYR A 904 PHE 0.029 0.001 PHE A 133 TRP 0.022 0.001 TRP C 104 HIS 0.009 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (25627) covalent geometry : angle 0.62269 / 0.30 (34864) SS BOND : bond 0.00295 / 0.19 ( 36) SS BOND : angle 1.44740 / 1.00 ( 72) hydrogen bonds : bond 0.03810 / 2.53 ( 920) hydrogen bonds : angle 5.15106 / 3.50 ( 2508) link_NAG-ASN : bond 0.00413 / 0.31 ( 27) link_NAG-ASN : angle 2.05367 / 1.36 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10720.68 seconds wall clock time: 182 minutes 41.43 seconds (10961.43 seconds total)