Starting phenix.real_space_refine on Mon Jun 23 13:11:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uza_26884/06_2025/7uza_26884.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uza_26884/06_2025/7uza_26884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uza_26884/06_2025/7uza_26884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uza_26884/06_2025/7uza_26884.map" model { file = "/net/cci-nas-00/data/ceres_data/7uza_26884/06_2025/7uza_26884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uza_26884/06_2025/7uza_26884.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 120 5.16 5 C 17180 2.51 5 N 4438 2.21 5 O 5254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26992 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 965 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 18.40, per 1000 atoms: 0.68 Number of scatterers: 26992 At special positions: 0 Unit cell: (158.912, 164.736, 196.352, 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 120 16.00 O 5254 8.00 N 4438 7.00 C 17180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A 282 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 61 " " NAG B1311 " - " ASN B 282 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 61 " " NAG C1312 " - " ASN C 282 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " Time building additional restraints: 7.52 Conformation dependent library (CDL) restraints added in 4.0 seconds 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6372 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 56 sheets defined 22.9% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.49 Creating SS restraints... Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.676A pdb=" N GLY A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.615A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) 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 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: 3.501A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.691A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.204A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.020A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.782A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.923A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.586A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 755 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.529A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.630A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.658A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.216A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.140A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.913A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 755 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.153A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.810A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.866A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.363A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 86 removed outlier: 3.924A pdb=" N THR H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.030A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.256A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.738A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.128A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.124A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 12.589A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.998A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 14.677A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 14.644A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.128A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.124A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 12.589A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 90 through 94 removed outlier: 6.224A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.548A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.122A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.693A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.703A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.496A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.331A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.354A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.562A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.001A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.479A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 90 through 94 removed outlier: 5.885A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 101 through 104 Processing sheet with id=AC5, first strand: chain 'B' and resid 116 through 121 removed outlier: 5.577A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR B 144 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TRP B 152 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 116 through 121 removed outlier: 7.251A pdb=" N LEU B 244 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N TYR B 145 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.341A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.709A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.717A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 392 " --> pdb=" O VAL B 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.571A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 727 removed outlier: 6.688A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 727 Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1081 through 1083 removed outlier: 4.928A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.309A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.019A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.736A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.119A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 144 through 146 removed outlier: 3.544A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.433A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.759A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.386A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.634A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF5, first strand: chain 'C' and resid 1081 through 1083 removed outlier: 6.781A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.581A pdb=" N GLN H 5 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS H 24 " --> pdb=" O GLN H 5 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.050A pdb=" N MET H 39 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY H 54 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TRP H 41 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TRP H 52 " --> pdb=" O TRP H 41 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS H 43 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU H 50 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG H 45 " --> pdb=" O GLN H 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 20 through 21 Processing sheet with id=AF9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.674A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE L 21 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS L 23 " --> pdb=" O PHE L 87 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE L 87 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 11 through 12 removed outlier: 7.116A pdb=" N LEU L 11 " --> pdb=" O GLU L 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'L' and resid 51 through 54 removed outlier: 6.642A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR L 103 " --> pdb=" O TYR L 42 " (cutoff:3.500A) 1034 hydrogen bonds defined for protein. 2838 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.83 Time building geometry restraints manager: 8.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8509 1.34 - 1.46: 5878 1.46 - 1.58: 13083 1.58 - 1.70: 0 1.70 - 1.82: 155 Bond restraints: 27625 Sorted by residual: bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.509 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" N VAL C 705 " pdb=" CA VAL C 705 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.27e-02 6.20e+03 7.74e+00 bond pdb=" N GLU C1072 " pdb=" CA GLU C1072 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.21e-02 6.83e+03 6.55e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.40e+00 ... (remaining 27620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 36770 1.82 - 3.63: 777 3.63 - 5.45: 66 5.45 - 7.26: 12 7.26 - 9.08: 6 Bond angle restraints: 37631 Sorted by residual: angle pdb=" C ASN C1074 " pdb=" CA ASN C1074 " pdb=" CB ASN C1074 " ideal model delta sigma weight residual 109.48 116.83 -7.35 1.68e+00 3.54e-01 1.91e+01 angle pdb=" C ALA L 9 " pdb=" CA ALA L 9 " pdb=" CB ALA L 9 " ideal model delta sigma weight residual 116.34 110.89 5.45 1.40e+00 5.10e-01 1.52e+01 angle pdb=" C SER A1030 " pdb=" N GLU A1031 " pdb=" CA GLU A1031 " ideal model delta sigma weight residual 122.67 116.61 6.06 1.59e+00 3.96e-01 1.45e+01 angle pdb=" N GLY H 49 " pdb=" CA GLY H 49 " pdb=" C GLY H 49 " ideal model delta sigma weight residual 111.36 115.10 -3.74 1.17e+00 7.31e-01 1.02e+01 angle pdb=" N ASP L 114 " pdb=" CA ASP L 114 " pdb=" C ASP L 114 " ideal model delta sigma weight residual 109.81 116.51 -6.70 2.21e+00 2.05e-01 9.18e+00 ... (remaining 37626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.32: 16061 24.32 - 48.65: 717 48.65 - 72.97: 83 72.97 - 97.30: 18 97.30 - 121.62: 20 Dihedral angle restraints: 16899 sinusoidal: 6979 harmonic: 9920 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -150.21 64.21 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 104 " pdb=" CB CYS L 104 " ideal model delta sinusoidal sigma weight residual 93.00 141.58 -48.58 1 1.00e+01 1.00e-02 3.25e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -132.63 46.63 1 1.00e+01 1.00e-02 3.01e+01 ... (remaining 16896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4161 0.099 - 0.199: 190 0.199 - 0.298: 7 0.298 - 0.397: 2 0.397 - 0.496: 1 Chirality restraints: 4361 Sorted by residual: chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.16e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 4358 not shown) Planarity restraints: 4869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1308 " 0.205 2.00e-02 2.50e+03 1.70e-01 3.61e+02 pdb=" C7 NAG C1308 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG C1308 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG C1308 " -0.277 2.00e-02 2.50e+03 pdb=" O7 NAG C1308 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 801 " -0.006 2.00e-02 2.50e+03 3.30e-02 1.36e+01 pdb=" CG ASN C 801 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN C 801 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN C 801 " 0.026 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 41 " 0.016 2.00e-02 2.50e+03 1.63e-02 6.65e+00 pdb=" CG TRP L 41 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP L 41 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP L 41 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP L 41 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP L 41 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 41 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 41 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 41 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP L 41 " -0.005 2.00e-02 2.50e+03 ... (remaining 4866 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 650 2.69 - 3.24: 27182 3.24 - 3.80: 43547 3.80 - 4.35: 57861 4.35 - 4.90: 95394 Nonbonded interactions: 224634 Sorted by model distance: nonbonded pdb=" OD1 ASP A 568 " pdb=" N ILE A 569 " model vdw 2.139 3.120 nonbonded pdb=" OE1 GLU B 819 " pdb=" OG SER B1055 " model vdw 2.170 3.040 nonbonded pdb=" O GLU C 780 " pdb=" NE2 GLN C 784 " model vdw 2.193 3.120 nonbonded pdb=" O THR A1116 " pdb=" OG1 THR A1120 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASN C 801 " pdb=" ND2 ASN C 928 " model vdw 2.201 3.120 ... (remaining 224629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 26 through 1147 or resid 1301 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 6.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.200 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 76.170 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.280 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: 0.040 Load rotamer database and sin/cos tables:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 27701 Z= 0.199 Angle : 0.648 12.535 37821 Z= 0.341 Chirality : 0.046 0.496 4361 Planarity : 0.004 0.170 4833 Dihedral : 13.777 121.624 10413 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.03 % Allowed : 0.17 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3369 helix: 1.38 (0.19), residues: 673 sheet: 0.00 (0.19), residues: 710 loop : -0.64 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP L 41 HIS 0.006 0.001 HIS H 57 PHE 0.029 0.002 PHE C 802 TYR 0.021 0.002 TYR C1138 ARG 0.007 0.000 ARG L 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 36) link_NAG-ASN : angle 3.23368 ( 108) link_BETA1-4 : bond 0.00121 ( 2) link_BETA1-4 : angle 0.85690 ( 6) hydrogen bonds : bond 0.21396 ( 1004) hydrogen bonds : angle 9.16299 ( 2838) SS BOND : bond 0.00242 ( 38) SS BOND : angle 1.00754 ( 76) covalent geometry : bond 0.00409 (27625) covalent geometry : angle 0.62440 (37631) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8408 (pp30) cc_final: 0.8022 (pp30) REVERT: A 351 TYR cc_start: 0.8347 (p90) cc_final: 0.7914 (p90) REVERT: A 584 ILE cc_start: 0.8987 (mm) cc_final: 0.8559 (tp) REVERT: A 663 ASP cc_start: 0.8009 (m-30) cc_final: 0.7411 (m-30) REVERT: B 106 PHE cc_start: 0.6849 (p90) cc_final: 0.6599 (p90) REVERT: B 229 LEU cc_start: 0.8528 (mt) cc_final: 0.8161 (tt) REVERT: B 313 TYR cc_start: 0.7685 (m-80) cc_final: 0.7316 (m-80) REVERT: B 420 ASP cc_start: 0.8199 (t70) cc_final: 0.7771 (t0) REVERT: B 501 ASN cc_start: 0.8262 (m110) cc_final: 0.7928 (m-40) REVERT: B 697 MET cc_start: 0.7325 (ptm) cc_final: 0.7067 (ptm) REVERT: B 900 MET cc_start: 0.6906 (mtm) cc_final: 0.6595 (mtp) REVERT: B 1141 LEU cc_start: 0.8652 (mm) cc_final: 0.8317 (tp) REVERT: H 40 HIS cc_start: 0.9306 (m170) cc_final: 0.8987 (m170) REVERT: H 51 GLU cc_start: 0.8448 (pp20) cc_final: 0.7894 (pp20) REVERT: H 88 TYR cc_start: 0.8881 (m-80) cc_final: 0.8140 (m-80) REVERT: H 89 MET cc_start: 0.7326 (ppp) cc_final: 0.7098 (ppp) REVERT: H 113 ASP cc_start: 0.7780 (m-30) cc_final: 0.7168 (m-30) REVERT: L 24 ARG cc_start: 0.8805 (ptp-110) cc_final: 0.7844 (ttm110) REVERT: L 85 THR cc_start: 0.8694 (t) cc_final: 0.8124 (t) outliers start: 1 outliers final: 0 residues processed: 315 average time/residue: 0.3773 time to fit residues: 197.6612 Evaluate side-chains 242 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 3.9990 chunk 256 optimal weight: 20.0000 chunk 142 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 306 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 218 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 907 ASN B 913 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 969 ASN H 59 ASN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.162379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.102677 restraints weight = 47427.240| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.75 r_work: 0.3398 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27701 Z= 0.151 Angle : 0.629 11.719 37821 Z= 0.312 Chirality : 0.047 0.484 4361 Planarity : 0.004 0.043 4833 Dihedral : 9.104 112.575 4455 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.62 % Allowed : 6.36 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3369 helix: 1.43 (0.19), residues: 692 sheet: -0.01 (0.19), residues: 752 loop : -0.66 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 41 HIS 0.005 0.001 HIS C1048 PHE 0.029 0.002 PHE A 168 TYR 0.025 0.001 TYR C 248 ARG 0.004 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 36) link_NAG-ASN : angle 3.07322 ( 108) link_BETA1-4 : bond 0.00204 ( 2) link_BETA1-4 : angle 0.90412 ( 6) hydrogen bonds : bond 0.04880 ( 1004) hydrogen bonds : angle 6.89226 ( 2838) SS BOND : bond 0.00316 ( 38) SS BOND : angle 1.13947 ( 76) covalent geometry : bond 0.00337 (27625) covalent geometry : angle 0.60612 (37631) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 274 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8481 (pp30) cc_final: 0.8022 (pp30) REVERT: A 86 PHE cc_start: 0.4510 (t80) cc_final: 0.4129 (t80) REVERT: A 351 TYR cc_start: 0.8327 (p90) cc_final: 0.7905 (p90) REVERT: A 663 ASP cc_start: 0.8149 (m-30) cc_final: 0.7549 (m-30) REVERT: B 55 PHE cc_start: 0.7175 (m-10) cc_final: 0.6492 (m-10) REVERT: B 313 TYR cc_start: 0.7767 (m-80) cc_final: 0.7358 (m-80) REVERT: B 403 ARG cc_start: 0.6984 (ttp80) cc_final: 0.6112 (ttp80) REVERT: B 501 ASN cc_start: 0.8272 (m110) cc_final: 0.7864 (m110) REVERT: B 571 ASP cc_start: 0.7287 (m-30) cc_final: 0.6980 (t0) REVERT: B 578 ASP cc_start: 0.8542 (t70) cc_final: 0.8270 (t70) REVERT: B 697 MET cc_start: 0.7561 (ptm) cc_final: 0.7215 (ptm) REVERT: B 740 MET cc_start: 0.8769 (tpp) cc_final: 0.8531 (tpt) REVERT: B 902 MET cc_start: 0.7825 (tpt) cc_final: 0.7150 (tpt) REVERT: B 1141 LEU cc_start: 0.8617 (mm) cc_final: 0.8121 (tp) REVERT: B 1142 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8788 (mm110) REVERT: C 988 GLU cc_start: 0.6942 (pm20) cc_final: 0.6711 (pm20) REVERT: H 6 GLN cc_start: 0.3827 (mm-40) cc_final: 0.3611 (mm-40) REVERT: H 43 LYS cc_start: 0.4673 (pptt) cc_final: 0.4462 (ptmm) REVERT: H 113 ASP cc_start: 0.7557 (m-30) cc_final: 0.7263 (m-30) REVERT: L 24 ARG cc_start: 0.8468 (ptp-110) cc_final: 0.8236 (ttm110) REVERT: L 51 LYS cc_start: 0.8672 (tppt) cc_final: 0.8302 (tttm) REVERT: L 53 LEU cc_start: 0.7790 (mp) cc_final: 0.7538 (mp) REVERT: L 116 PHE cc_start: 0.8915 (m-80) cc_final: 0.8208 (m-80) outliers start: 18 outliers final: 5 residues processed: 284 average time/residue: 0.4841 time to fit residues: 232.6011 Evaluate side-chains 245 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 240 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain L residue 21 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 299 optimal weight: 7.9990 chunk 217 optimal weight: 30.0000 chunk 118 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 315 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 250 optimal weight: 50.0000 chunk 324 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B1011 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C1088 HIS H 59 ASN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.156591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.095247 restraints weight = 47636.191| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.70 r_work: 0.3276 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 27701 Z= 0.305 Angle : 0.715 12.661 37821 Z= 0.355 Chirality : 0.050 0.481 4361 Planarity : 0.004 0.043 4833 Dihedral : 8.137 111.181 4455 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.64 % Allowed : 9.09 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3369 helix: 0.94 (0.19), residues: 690 sheet: -0.20 (0.18), residues: 773 loop : -0.77 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 353 HIS 0.008 0.002 HIS L 105 PHE 0.036 0.003 PHE A1121 TYR 0.029 0.002 TYR C1067 ARG 0.009 0.001 ARG L 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 36) link_NAG-ASN : angle 3.31626 ( 108) link_BETA1-4 : bond 0.00087 ( 2) link_BETA1-4 : angle 1.03524 ( 6) hydrogen bonds : bond 0.05140 ( 1004) hydrogen bonds : angle 6.83576 ( 2838) SS BOND : bond 0.00648 ( 38) SS BOND : angle 1.52299 ( 76) covalent geometry : bond 0.00712 (27625) covalent geometry : angle 0.69098 (37631) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 253 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8632 (pp30) cc_final: 0.8061 (pp30) REVERT: A 160 TYR cc_start: 0.7764 (p90) cc_final: 0.7481 (p90) REVERT: A 368 LEU cc_start: 0.8185 (mm) cc_final: 0.7891 (tp) REVERT: A 390 LEU cc_start: 0.3536 (OUTLIER) cc_final: 0.3240 (pp) REVERT: A 508 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8648 (t80) REVERT: A 740 MET cc_start: 0.8032 (tpt) cc_final: 0.7059 (mmt) REVERT: B 237 ARG cc_start: 0.7323 (mmm-85) cc_final: 0.6947 (mmm-85) REVERT: B 313 TYR cc_start: 0.8144 (m-80) cc_final: 0.7578 (m-80) REVERT: B 403 ARG cc_start: 0.6887 (ttp80) cc_final: 0.6101 (ttp80) REVERT: B 420 ASP cc_start: 0.8376 (t70) cc_final: 0.8088 (t0) REVERT: B 501 ASN cc_start: 0.8264 (m110) cc_final: 0.7875 (m110) REVERT: B 571 ASP cc_start: 0.7380 (m-30) cc_final: 0.7176 (t0) REVERT: B 697 MET cc_start: 0.7648 (ptm) cc_final: 0.7195 (ptm) REVERT: B 823 PHE cc_start: 0.7769 (m-80) cc_final: 0.7284 (m-80) REVERT: B 900 MET cc_start: 0.7092 (mtm) cc_final: 0.6878 (mtp) REVERT: B 1141 LEU cc_start: 0.8608 (mm) cc_final: 0.8113 (tp) REVERT: B 1142 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8802 (mm110) REVERT: H 41 TRP cc_start: 0.7060 (m100) cc_final: 0.6557 (m100) REVERT: H 67 TYR cc_start: 0.5617 (m-80) cc_final: 0.5372 (m-80) REVERT: H 88 TYR cc_start: 0.8893 (m-80) cc_final: 0.8262 (m-80) REVERT: H 113 ASP cc_start: 0.7560 (m-30) cc_final: 0.7196 (m-30) REVERT: L 24 ARG cc_start: 0.8617 (ptp-110) cc_final: 0.7947 (ttp-110) REVERT: L 29 VAL cc_start: 0.5955 (OUTLIER) cc_final: 0.5721 (m) REVERT: L 118 PHE cc_start: 0.8495 (m-80) cc_final: 0.8014 (m-80) outliers start: 48 outliers final: 25 residues processed: 288 average time/residue: 0.3506 time to fit residues: 168.8761 Evaluate side-chains 249 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 54 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 250 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 88 optimal weight: 0.0970 chunk 148 optimal weight: 7.9990 chunk 183 optimal weight: 0.6980 chunk 291 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 chunk 279 optimal weight: 0.6980 chunk 312 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 315 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 149 ASN ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.161030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.101151 restraints weight = 47754.027| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.75 r_work: 0.3377 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27701 Z= 0.130 Angle : 0.598 12.117 37821 Z= 0.295 Chirality : 0.046 0.487 4361 Planarity : 0.004 0.050 4833 Dihedral : 7.260 106.977 4455 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.30 % Allowed : 10.50 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3369 helix: 1.44 (0.19), residues: 684 sheet: -0.26 (0.18), residues: 772 loop : -0.78 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 353 HIS 0.018 0.001 HIS A 519 PHE 0.023 0.002 PHE C 65 TYR 0.020 0.001 TYR A 91 ARG 0.005 0.000 ARG L 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 36) link_NAG-ASN : angle 3.04000 ( 108) link_BETA1-4 : bond 0.00290 ( 2) link_BETA1-4 : angle 1.08964 ( 6) hydrogen bonds : bond 0.04214 ( 1004) hydrogen bonds : angle 6.32732 ( 2838) SS BOND : bond 0.00418 ( 38) SS BOND : angle 1.10657 ( 76) covalent geometry : bond 0.00281 (27625) covalent geometry : angle 0.57476 (37631) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8502 (pp30) cc_final: 0.8003 (pp30) REVERT: A 160 TYR cc_start: 0.7762 (p90) cc_final: 0.7446 (p90) REVERT: A 314 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 368 LEU cc_start: 0.8150 (mm) cc_final: 0.7888 (tp) REVERT: A 386 LYS cc_start: 0.8712 (mmmm) cc_final: 0.8457 (mmmm) REVERT: A 508 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8590 (t80) REVERT: A 740 MET cc_start: 0.7992 (tpt) cc_final: 0.7032 (mmt) REVERT: B 55 PHE cc_start: 0.7281 (m-10) cc_final: 0.6650 (m-10) REVERT: B 170 TYR cc_start: 0.7958 (t80) cc_final: 0.7685 (t80) REVERT: B 313 TYR cc_start: 0.7911 (m-80) cc_final: 0.7406 (m-80) REVERT: B 355 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7219 (ttp80) REVERT: B 420 ASP cc_start: 0.8358 (t70) cc_final: 0.7939 (t0) REVERT: B 501 ASN cc_start: 0.8237 (m110) cc_final: 0.7828 (m110) REVERT: B 571 ASP cc_start: 0.7234 (m-30) cc_final: 0.6960 (t0) REVERT: B 578 ASP cc_start: 0.8546 (t70) cc_final: 0.8185 (t70) REVERT: B 697 MET cc_start: 0.7602 (ptm) cc_final: 0.7189 (ptm) REVERT: B 916 LEU cc_start: 0.7289 (tp) cc_final: 0.7011 (tp) REVERT: B 983 ARG cc_start: 0.8868 (ttm110) cc_final: 0.8533 (ttm110) REVERT: B 1141 LEU cc_start: 0.8622 (mm) cc_final: 0.8132 (tp) REVERT: B 1142 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8805 (mm110) REVERT: C 988 GLU cc_start: 0.7143 (pm20) cc_final: 0.6835 (pm20) REVERT: H 41 TRP cc_start: 0.6904 (m100) cc_final: 0.6534 (m100) REVERT: H 113 ASP cc_start: 0.7735 (m-30) cc_final: 0.7335 (m-30) REVERT: L 24 ARG cc_start: 0.8632 (ptp-110) cc_final: 0.8157 (ttm110) REVERT: L 29 VAL cc_start: 0.5799 (OUTLIER) cc_final: 0.5522 (m) outliers start: 38 outliers final: 19 residues processed: 293 average time/residue: 0.3443 time to fit residues: 167.7259 Evaluate side-chains 257 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 235 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 88 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 229 optimal weight: 0.0980 chunk 81 optimal weight: 0.0970 chunk 136 optimal weight: 0.8980 chunk 221 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 901 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN L 44 GLN ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.161241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.101456 restraints weight = 47622.804| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.74 r_work: 0.3379 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27701 Z= 0.129 Angle : 0.594 11.990 37821 Z= 0.290 Chirality : 0.046 0.475 4361 Planarity : 0.004 0.053 4833 Dihedral : 6.940 105.515 4455 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.74 % Allowed : 11.35 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3369 helix: 1.62 (0.19), residues: 681 sheet: -0.27 (0.18), residues: 757 loop : -0.83 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 353 HIS 0.004 0.001 HIS C1048 PHE 0.028 0.001 PHE C 220 TYR 0.019 0.001 TYR C 248 ARG 0.005 0.000 ARG L 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 36) link_NAG-ASN : angle 2.93356 ( 108) link_BETA1-4 : bond 0.00230 ( 2) link_BETA1-4 : angle 0.97016 ( 6) hydrogen bonds : bond 0.04079 ( 1004) hydrogen bonds : angle 6.16473 ( 2838) SS BOND : bond 0.00477 ( 38) SS BOND : angle 1.14646 ( 76) covalent geometry : bond 0.00293 (27625) covalent geometry : angle 0.57185 (37631) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 256 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8482 (pp30) cc_final: 0.7988 (pp30) REVERT: A 104 TRP cc_start: 0.6205 (m-90) cc_final: 0.5877 (m-10) REVERT: A 153 MET cc_start: 0.8536 (mpp) cc_final: 0.8312 (pmm) REVERT: A 160 TYR cc_start: 0.7837 (p90) cc_final: 0.7455 (p90) REVERT: A 314 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7826 (tm-30) REVERT: A 368 LEU cc_start: 0.8145 (mm) cc_final: 0.7880 (tp) REVERT: A 386 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8522 (mmmt) REVERT: A 508 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8583 (t80) REVERT: A 740 MET cc_start: 0.7994 (tpt) cc_final: 0.7028 (mmt) REVERT: B 55 PHE cc_start: 0.7595 (m-10) cc_final: 0.6832 (m-10) REVERT: B 101 ILE cc_start: 0.8181 (mp) cc_final: 0.7888 (mm) REVERT: B 273 ARG cc_start: 0.7357 (mmm-85) cc_final: 0.6660 (mmm-85) REVERT: B 313 TYR cc_start: 0.7935 (m-80) cc_final: 0.7429 (m-80) REVERT: B 403 ARG cc_start: 0.7051 (ttp80) cc_final: 0.6629 (ttp80) REVERT: B 449 TYR cc_start: 0.7995 (m-80) cc_final: 0.7780 (m-80) REVERT: B 501 ASN cc_start: 0.8253 (m110) cc_final: 0.7852 (m110) REVERT: B 571 ASP cc_start: 0.7188 (m-30) cc_final: 0.6952 (t0) REVERT: B 697 MET cc_start: 0.7630 (ptm) cc_final: 0.7214 (ptm) REVERT: B 983 ARG cc_start: 0.8855 (ttm110) cc_final: 0.8481 (ttm110) REVERT: B 1141 LEU cc_start: 0.8620 (mm) cc_final: 0.8161 (tp) REVERT: C 318 PHE cc_start: 0.7917 (t80) cc_final: 0.7656 (t80) REVERT: C 988 GLU cc_start: 0.7078 (pm20) cc_final: 0.6859 (pm20) REVERT: C 1127 ASP cc_start: 0.8418 (t0) cc_final: 0.7569 (m-30) REVERT: H 6 GLN cc_start: 0.4182 (mm-40) cc_final: 0.3698 (mm-40) REVERT: H 41 TRP cc_start: 0.6952 (m100) cc_final: 0.6072 (m100) REVERT: H 45 ARG cc_start: 0.5447 (mpp80) cc_final: 0.5167 (mpp80) REVERT: H 89 MET cc_start: 0.6497 (ppp) cc_final: 0.6294 (ppp) REVERT: H 113 ASP cc_start: 0.7687 (m-30) cc_final: 0.7335 (m-30) REVERT: L 24 ARG cc_start: 0.8597 (ptp-110) cc_final: 0.7597 (mtp-110) REVERT: L 51 LYS cc_start: 0.8942 (tppt) cc_final: 0.8378 (tttm) outliers start: 51 outliers final: 35 residues processed: 291 average time/residue: 0.4222 time to fit residues: 203.2537 Evaluate side-chains 266 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 94 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 64 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 49 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 309 optimal weight: 0.2980 chunk 297 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 254 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.161383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.101617 restraints weight = 47701.846| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.75 r_work: 0.3382 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27701 Z= 0.129 Angle : 0.583 11.802 37821 Z= 0.286 Chirality : 0.045 0.468 4361 Planarity : 0.003 0.054 4833 Dihedral : 6.747 106.456 4455 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.61 % Allowed : 12.27 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3369 helix: 1.59 (0.19), residues: 685 sheet: -0.21 (0.19), residues: 736 loop : -0.83 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 353 HIS 0.005 0.001 HIS H 57 PHE 0.025 0.001 PHE A 65 TYR 0.020 0.001 TYR C 248 ARG 0.005 0.000 ARG L 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 36) link_NAG-ASN : angle 2.86745 ( 108) link_BETA1-4 : bond 0.00179 ( 2) link_BETA1-4 : angle 0.97456 ( 6) hydrogen bonds : bond 0.03991 ( 1004) hydrogen bonds : angle 6.04781 ( 2838) SS BOND : bond 0.00337 ( 38) SS BOND : angle 1.05445 ( 76) covalent geometry : bond 0.00295 (27625) covalent geometry : angle 0.56206 (37631) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 254 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8469 (pp30) cc_final: 0.7978 (pp30) REVERT: A 104 TRP cc_start: 0.6187 (m-90) cc_final: 0.5848 (m-10) REVERT: A 153 MET cc_start: 0.8544 (mpp) cc_final: 0.8300 (pmm) REVERT: A 160 TYR cc_start: 0.7822 (p90) cc_final: 0.7465 (p90) REVERT: A 314 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7821 (tm-30) REVERT: A 368 LEU cc_start: 0.8148 (mm) cc_final: 0.7876 (tp) REVERT: A 386 LYS cc_start: 0.8704 (mmmm) cc_final: 0.8486 (mmmm) REVERT: A 464 PHE cc_start: 0.6993 (m-10) cc_final: 0.6757 (m-10) REVERT: A 508 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8571 (t80) REVERT: A 1031 GLU cc_start: 0.7575 (pm20) cc_final: 0.7356 (pt0) REVERT: B 55 PHE cc_start: 0.7715 (m-10) cc_final: 0.6783 (m-10) REVERT: B 101 ILE cc_start: 0.8202 (mp) cc_final: 0.7941 (mm) REVERT: B 273 ARG cc_start: 0.7323 (mmm-85) cc_final: 0.6597 (mmm-85) REVERT: B 313 TYR cc_start: 0.7937 (m-80) cc_final: 0.7416 (m-80) REVERT: B 449 TYR cc_start: 0.7997 (m-80) cc_final: 0.7436 (m-80) REVERT: B 501 ASN cc_start: 0.8264 (m110) cc_final: 0.7853 (m110) REVERT: B 571 ASP cc_start: 0.7121 (m-30) cc_final: 0.6904 (t0) REVERT: B 697 MET cc_start: 0.7612 (ptm) cc_final: 0.7210 (ptm) REVERT: B 1141 LEU cc_start: 0.8605 (mm) cc_final: 0.8208 (tp) REVERT: C 318 PHE cc_start: 0.7958 (t80) cc_final: 0.7672 (t80) REVERT: C 988 GLU cc_start: 0.7104 (pm20) cc_final: 0.6866 (pm20) REVERT: C 1082 CYS cc_start: 0.7559 (t) cc_final: 0.7289 (t) REVERT: C 1127 ASP cc_start: 0.8400 (t0) cc_final: 0.7515 (m-30) REVERT: H 6 GLN cc_start: 0.4121 (mm-40) cc_final: 0.3686 (mm-40) REVERT: H 41 TRP cc_start: 0.6703 (m100) cc_final: 0.6346 (m100) REVERT: H 45 ARG cc_start: 0.5583 (mpp80) cc_final: 0.5110 (mpp80) REVERT: H 51 GLU cc_start: 0.8320 (pp20) cc_final: 0.8052 (pm20) REVERT: H 88 TYR cc_start: 0.8747 (m-80) cc_final: 0.8196 (m-80) REVERT: H 113 ASP cc_start: 0.7748 (m-30) cc_final: 0.7297 (m-30) REVERT: L 24 ARG cc_start: 0.8555 (ptp-110) cc_final: 0.7595 (mtp-110) REVERT: L 51 LYS cc_start: 0.8985 (tppt) cc_final: 0.8441 (tttm) outliers start: 47 outliers final: 35 residues processed: 287 average time/residue: 0.3753 time to fit residues: 180.3063 Evaluate side-chains 266 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 94 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 234 optimal weight: 4.9990 chunk 226 optimal weight: 10.0000 chunk 21 optimal weight: 40.0000 chunk 7 optimal weight: 10.0000 chunk 192 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 220 optimal weight: 30.0000 chunk 337 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN L 44 GLN ** L 105 HIS ** 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 = 0.4367 r_free = 0.4367 target = 0.158338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.097539 restraints weight = 47682.663| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.71 r_work: 0.3314 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27701 Z= 0.215 Angle : 0.632 11.875 37821 Z= 0.312 Chirality : 0.047 0.457 4361 Planarity : 0.004 0.055 4833 Dihedral : 6.825 107.630 4455 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.95 % Allowed : 12.99 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3369 helix: 1.32 (0.19), residues: 684 sheet: -0.33 (0.19), residues: 743 loop : -0.89 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP L 41 HIS 0.005 0.001 HIS A 66 PHE 0.027 0.002 PHE A1121 TYR 0.022 0.002 TYR C1067 ARG 0.005 0.000 ARG L 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 36) link_NAG-ASN : angle 2.91378 ( 108) link_BETA1-4 : bond 0.00142 ( 2) link_BETA1-4 : angle 1.01717 ( 6) hydrogen bonds : bond 0.04360 ( 1004) hydrogen bonds : angle 6.21383 ( 2838) SS BOND : bond 0.00422 ( 38) SS BOND : angle 1.22129 ( 76) covalent geometry : bond 0.00499 (27625) covalent geometry : angle 0.61174 (37631) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 3.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8575 (pp30) cc_final: 0.8043 (pp30) REVERT: A 104 TRP cc_start: 0.6292 (m-90) cc_final: 0.6008 (m-10) REVERT: A 160 TYR cc_start: 0.7849 (p90) cc_final: 0.7477 (p90) REVERT: A 368 LEU cc_start: 0.8171 (mm) cc_final: 0.7905 (tp) REVERT: A 386 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8444 (mmmm) REVERT: A 508 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.8571 (t80) REVERT: A 740 MET cc_start: 0.7953 (tpt) cc_final: 0.7045 (mmt) REVERT: A 878 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8010 (mp) REVERT: B 55 PHE cc_start: 0.7958 (m-10) cc_final: 0.6992 (m-10) REVERT: B 237 ARG cc_start: 0.7332 (mmm-85) cc_final: 0.6923 (mmm-85) REVERT: B 313 TYR cc_start: 0.8076 (m-80) cc_final: 0.7487 (m-80) REVERT: B 403 ARG cc_start: 0.7083 (ttp80) cc_final: 0.6042 (ttp80) REVERT: B 449 TYR cc_start: 0.8011 (m-80) cc_final: 0.7434 (m-80) REVERT: B 501 ASN cc_start: 0.8235 (m110) cc_final: 0.7827 (m110) REVERT: B 571 ASP cc_start: 0.7203 (m-30) cc_final: 0.6966 (t0) REVERT: B 697 MET cc_start: 0.7678 (ptm) cc_final: 0.7272 (ptm) REVERT: B 823 PHE cc_start: 0.7620 (m-80) cc_final: 0.7150 (m-80) REVERT: B 1141 LEU cc_start: 0.8613 (mm) cc_final: 0.8168 (tp) REVERT: B 1142 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8789 (mm110) REVERT: C 318 PHE cc_start: 0.7978 (t80) cc_final: 0.7713 (t80) REVERT: C 1082 CYS cc_start: 0.7648 (t) cc_final: 0.7388 (t) REVERT: C 1089 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: C 1127 ASP cc_start: 0.8403 (t0) cc_final: 0.7510 (m-30) REVERT: H 5 GLN cc_start: 0.7980 (mp10) cc_final: 0.7573 (mp10) REVERT: H 6 GLN cc_start: 0.4024 (mm-40) cc_final: 0.3673 (tp40) REVERT: H 43 LYS cc_start: 0.4343 (pttm) cc_final: 0.3472 (pttp) REVERT: H 113 ASP cc_start: 0.7758 (m-30) cc_final: 0.7360 (m-30) REVERT: L 24 ARG cc_start: 0.8561 (ptp-110) cc_final: 0.7561 (mtp-110) REVERT: L 51 LYS cc_start: 0.9003 (tppt) cc_final: 0.8450 (tttm) outliers start: 57 outliers final: 41 residues processed: 279 average time/residue: 0.4521 time to fit residues: 212.0813 Evaluate side-chains 271 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 94 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 271 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 118 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 233 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 211 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 chunk 306 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.160372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.100385 restraints weight = 47501.684| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.74 r_work: 0.3362 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27701 Z= 0.133 Angle : 0.599 11.685 37821 Z= 0.292 Chirality : 0.046 0.461 4361 Planarity : 0.004 0.053 4833 Dihedral : 6.582 105.694 4455 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.61 % Allowed : 13.64 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3369 helix: 1.51 (0.19), residues: 689 sheet: -0.27 (0.19), residues: 730 loop : -0.88 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP L 41 HIS 0.004 0.001 HIS C1048 PHE 0.019 0.001 PHE C 65 TYR 0.021 0.001 TYR C 248 ARG 0.008 0.000 ARG L 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 36) link_NAG-ASN : angle 2.79333 ( 108) link_BETA1-4 : bond 0.00143 ( 2) link_BETA1-4 : angle 0.92397 ( 6) hydrogen bonds : bond 0.04023 ( 1004) hydrogen bonds : angle 6.00584 ( 2838) SS BOND : bond 0.00260 ( 38) SS BOND : angle 1.01937 ( 76) covalent geometry : bond 0.00301 (27625) covalent geometry : angle 0.57917 (37631) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8514 (pp30) cc_final: 0.7995 (pp30) REVERT: A 104 TRP cc_start: 0.6280 (m-90) cc_final: 0.5860 (m-10) REVERT: A 153 MET cc_start: 0.8523 (mpp) cc_final: 0.8294 (pmm) REVERT: A 160 TYR cc_start: 0.7801 (p90) cc_final: 0.7434 (p90) REVERT: A 368 LEU cc_start: 0.8153 (mm) cc_final: 0.7927 (tp) REVERT: A 386 LYS cc_start: 0.8881 (mmmm) cc_final: 0.8656 (mmmt) REVERT: A 400 PHE cc_start: 0.8820 (p90) cc_final: 0.8278 (p90) REVERT: A 428 ASP cc_start: 0.7830 (t0) cc_final: 0.7626 (p0) REVERT: A 508 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.8557 (t80) REVERT: A 740 MET cc_start: 0.7880 (tpt) cc_final: 0.6964 (mmt) REVERT: A 878 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7924 (mp) REVERT: B 55 PHE cc_start: 0.7888 (m-10) cc_final: 0.6990 (m-10) REVERT: B 313 TYR cc_start: 0.8003 (m-80) cc_final: 0.7461 (m-80) REVERT: B 403 ARG cc_start: 0.7060 (ttp80) cc_final: 0.6725 (ttp80) REVERT: B 449 TYR cc_start: 0.7984 (m-80) cc_final: 0.7443 (m-80) REVERT: B 501 ASN cc_start: 0.8266 (m110) cc_final: 0.7855 (m110) REVERT: B 697 MET cc_start: 0.7646 (ptm) cc_final: 0.7239 (ptm) REVERT: B 858 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8565 (pp) REVERT: B 983 ARG cc_start: 0.9183 (ttm110) cc_final: 0.8911 (ttm110) REVERT: B 1141 LEU cc_start: 0.8587 (mm) cc_final: 0.8143 (tp) REVERT: B 1142 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8779 (mm110) REVERT: C 318 PHE cc_start: 0.7952 (t80) cc_final: 0.7720 (t80) REVERT: C 1082 CYS cc_start: 0.7554 (t) cc_final: 0.7323 (t) REVERT: C 1127 ASP cc_start: 0.8380 (t0) cc_final: 0.7545 (m-30) REVERT: H 5 GLN cc_start: 0.7947 (mp10) cc_final: 0.7527 (mp10) REVERT: H 6 GLN cc_start: 0.4036 (mm-40) cc_final: 0.3740 (tp40) REVERT: H 45 ARG cc_start: 0.5853 (mpp80) cc_final: 0.5376 (mpp80) REVERT: H 113 ASP cc_start: 0.7784 (m-30) cc_final: 0.7383 (m-30) REVERT: L 24 ARG cc_start: 0.8529 (ptp-110) cc_final: 0.7517 (mtp-110) REVERT: L 51 LYS cc_start: 0.8995 (tppt) cc_final: 0.8459 (tttm) REVERT: L 118 PHE cc_start: 0.9025 (m-80) cc_final: 0.8514 (t80) outliers start: 47 outliers final: 39 residues processed: 276 average time/residue: 0.3373 time to fit residues: 157.4178 Evaluate side-chains 275 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 3.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 41 TRP Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 94 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 63 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 332 optimal weight: 20.0000 chunk 290 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 322 optimal weight: 0.7980 chunk 127 optimal weight: 20.0000 chunk 253 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C1010 GLN ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.156840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.095646 restraints weight = 47892.331| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.71 r_work: 0.3284 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 27701 Z= 0.257 Angle : 0.668 12.795 37821 Z= 0.329 Chirality : 0.048 0.463 4361 Planarity : 0.004 0.049 4833 Dihedral : 6.794 107.661 4455 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.68 % Allowed : 13.85 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3369 helix: 1.16 (0.19), residues: 683 sheet: -0.35 (0.19), residues: 721 loop : -0.95 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP L 41 HIS 0.004 0.001 HIS A1048 PHE 0.031 0.002 PHE B1121 TYR 0.024 0.002 TYR C1067 ARG 0.008 0.001 ARG L 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 36) link_NAG-ASN : angle 2.91057 ( 108) link_BETA1-4 : bond 0.00030 ( 2) link_BETA1-4 : angle 1.02458 ( 6) hydrogen bonds : bond 0.04544 ( 1004) hydrogen bonds : angle 6.28082 ( 2838) SS BOND : bond 0.00507 ( 38) SS BOND : angle 1.30010 ( 76) covalent geometry : bond 0.00600 (27625) covalent geometry : angle 0.64903 (37631) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 242 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8665 (pp30) cc_final: 0.8003 (pp30) REVERT: A 104 TRP cc_start: 0.6275 (m-90) cc_final: 0.5792 (m-10) REVERT: A 153 MET cc_start: 0.8558 (mpp) cc_final: 0.8301 (pmm) REVERT: A 160 TYR cc_start: 0.7841 (p90) cc_final: 0.7465 (p90) REVERT: A 321 GLN cc_start: 0.8165 (mp10) cc_final: 0.7891 (pm20) REVERT: A 368 LEU cc_start: 0.8178 (mm) cc_final: 0.7933 (tp) REVERT: A 386 LYS cc_start: 0.8875 (mmmm) cc_final: 0.8633 (mmmm) REVERT: A 400 PHE cc_start: 0.8842 (p90) cc_final: 0.8292 (p90) REVERT: A 428 ASP cc_start: 0.7864 (t0) cc_final: 0.7651 (p0) REVERT: A 508 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8631 (t80) REVERT: A 740 MET cc_start: 0.7966 (tpt) cc_final: 0.7044 (mmt) REVERT: A 878 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8019 (mp) REVERT: B 51 THR cc_start: 0.7227 (p) cc_final: 0.7024 (p) REVERT: B 55 PHE cc_start: 0.8102 (m-10) cc_final: 0.6974 (m-10) REVERT: B 237 ARG cc_start: 0.7305 (mmm-85) cc_final: 0.6930 (mmm-85) REVERT: B 313 TYR cc_start: 0.8194 (m-80) cc_final: 0.7581 (m-80) REVERT: B 403 ARG cc_start: 0.7183 (ttp80) cc_final: 0.6803 (ttp80) REVERT: B 501 ASN cc_start: 0.8238 (m110) cc_final: 0.7817 (m110) REVERT: B 697 MET cc_start: 0.7719 (ptm) cc_final: 0.7356 (ptm) REVERT: B 823 PHE cc_start: 0.7635 (m-80) cc_final: 0.7203 (m-80) REVERT: B 983 ARG cc_start: 0.9195 (ttm110) cc_final: 0.8978 (ttm110) REVERT: B 1141 LEU cc_start: 0.8596 (mm) cc_final: 0.8170 (tp) REVERT: C 318 PHE cc_start: 0.7946 (t80) cc_final: 0.7708 (t80) REVERT: C 1082 CYS cc_start: 0.7636 (t) cc_final: 0.7393 (t) REVERT: C 1127 ASP cc_start: 0.8401 (t0) cc_final: 0.7543 (m-30) REVERT: H 5 GLN cc_start: 0.7988 (mp10) cc_final: 0.7567 (mp10) REVERT: H 6 GLN cc_start: 0.4030 (mm-40) cc_final: 0.3707 (tp40) REVERT: H 67 TYR cc_start: 0.6001 (m-80) cc_final: 0.5602 (m-80) REVERT: H 113 ASP cc_start: 0.7761 (m-30) cc_final: 0.7408 (m-30) REVERT: L 24 ARG cc_start: 0.8519 (ptp-110) cc_final: 0.7915 (ttm110) REVERT: L 118 PHE cc_start: 0.9021 (m-80) cc_final: 0.8579 (t80) outliers start: 49 outliers final: 41 residues processed: 273 average time/residue: 0.4001 time to fit residues: 182.5251 Evaluate side-chains 276 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 5.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 94 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 3 optimal weight: 6.9990 chunk 314 optimal weight: 1.9990 chunk 297 optimal weight: 0.6980 chunk 228 optimal weight: 40.0000 chunk 307 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 330 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.159277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.098949 restraints weight = 47347.886| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.72 r_work: 0.3340 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27701 Z= 0.150 Angle : 0.618 11.852 37821 Z= 0.302 Chirality : 0.046 0.463 4361 Planarity : 0.004 0.052 4833 Dihedral : 6.548 105.231 4455 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.54 % Allowed : 14.19 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3369 helix: 1.36 (0.19), residues: 686 sheet: -0.37 (0.19), residues: 727 loop : -0.90 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP L 41 HIS 0.004 0.001 HIS C1048 PHE 0.021 0.002 PHE C 65 TYR 0.028 0.001 TYR C 248 ARG 0.007 0.000 ARG L 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 36) link_NAG-ASN : angle 2.78467 ( 108) link_BETA1-4 : bond 0.00010 ( 2) link_BETA1-4 : angle 0.88682 ( 6) hydrogen bonds : bond 0.04138 ( 1004) hydrogen bonds : angle 6.05442 ( 2838) SS BOND : bond 0.00300 ( 38) SS BOND : angle 1.10197 ( 76) covalent geometry : bond 0.00344 (27625) covalent geometry : angle 0.59906 (37631) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 245 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8624 (pp30) cc_final: 0.8000 (pp30) REVERT: A 104 TRP cc_start: 0.6113 (m-90) cc_final: 0.5691 (m-10) REVERT: A 118 LEU cc_start: 0.6670 (mp) cc_final: 0.6380 (pp) REVERT: A 153 MET cc_start: 0.8529 (mpp) cc_final: 0.8273 (pmm) REVERT: A 160 TYR cc_start: 0.7856 (p90) cc_final: 0.7483 (p90) REVERT: A 201 PHE cc_start: 0.7949 (t80) cc_final: 0.7525 (t80) REVERT: A 321 GLN cc_start: 0.8163 (mp10) cc_final: 0.7885 (pm20) REVERT: A 368 LEU cc_start: 0.8155 (mm) cc_final: 0.7917 (tp) REVERT: A 386 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8641 (mmmm) REVERT: A 508 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8617 (t80) REVERT: A 740 MET cc_start: 0.7911 (tpt) cc_final: 0.6987 (mmt) REVERT: A 878 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7904 (mp) REVERT: B 55 PHE cc_start: 0.7985 (m-10) cc_final: 0.6931 (m-10) REVERT: B 104 TRP cc_start: 0.6266 (m-90) cc_final: 0.5709 (m-90) REVERT: B 237 ARG cc_start: 0.7392 (mmm-85) cc_final: 0.6943 (mmm-85) REVERT: B 313 TYR cc_start: 0.8084 (m-80) cc_final: 0.7474 (m-80) REVERT: B 403 ARG cc_start: 0.7148 (ttp80) cc_final: 0.6746 (ttp80) REVERT: B 501 ASN cc_start: 0.8262 (m110) cc_final: 0.7869 (m110) REVERT: B 697 MET cc_start: 0.7689 (ptm) cc_final: 0.7278 (ptm) REVERT: B 823 PHE cc_start: 0.7558 (m-80) cc_final: 0.7131 (m-80) REVERT: B 858 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8600 (pp) REVERT: B 983 ARG cc_start: 0.9185 (ttm110) cc_final: 0.8964 (ttm110) REVERT: B 1141 LEU cc_start: 0.8586 (mm) cc_final: 0.8126 (tp) REVERT: C 318 PHE cc_start: 0.7879 (t80) cc_final: 0.7627 (t80) REVERT: C 1082 CYS cc_start: 0.7599 (t) cc_final: 0.7376 (t) REVERT: C 1127 ASP cc_start: 0.8401 (t0) cc_final: 0.7532 (m-30) REVERT: H 45 ARG cc_start: 0.6228 (mpp80) cc_final: 0.5614 (mpp80) REVERT: H 113 ASP cc_start: 0.7884 (m-30) cc_final: 0.7429 (m-30) REVERT: L 24 ARG cc_start: 0.8515 (ptp-110) cc_final: 0.7613 (mtp-110) REVERT: L 27 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8112 (mp0) outliers start: 45 outliers final: 39 residues processed: 274 average time/residue: 0.3458 time to fit residues: 159.8961 Evaluate side-chains 278 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 94 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 47 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 181 optimal weight: 0.1980 chunk 174 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.158748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.098244 restraints weight = 47602.535| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.73 r_work: 0.3325 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27701 Z= 0.171 Angle : 0.625 11.618 37821 Z= 0.306 Chirality : 0.046 0.460 4361 Planarity : 0.004 0.053 4833 Dihedral : 6.478 105.100 4455 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.47 % Allowed : 14.60 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3369 helix: 1.36 (0.19), residues: 686 sheet: -0.39 (0.19), residues: 711 loop : -0.92 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP L 41 HIS 0.003 0.001 HIS C1048 PHE 0.021 0.002 PHE C 65 TYR 0.024 0.001 TYR C 248 ARG 0.006 0.000 ARG L 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 36) link_NAG-ASN : angle 2.77036 ( 108) link_BETA1-4 : bond 0.00043 ( 2) link_BETA1-4 : angle 0.91506 ( 6) hydrogen bonds : bond 0.04162 ( 1004) hydrogen bonds : angle 6.05015 ( 2838) SS BOND : bond 0.00381 ( 38) SS BOND : angle 1.13634 ( 76) covalent geometry : bond 0.00395 (27625) covalent geometry : angle 0.60687 (37631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24574.20 seconds wall clock time: 426 minutes 50.33 seconds (25610.33 seconds total)