Starting phenix.real_space_refine on Thu Sep 18 16:39:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n7h_0356/09_2025/6n7h_0356_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7h_0356/09_2025/6n7h_0356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6n7h_0356/09_2025/6n7h_0356_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7h_0356/09_2025/6n7h_0356_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n7h_0356/09_2025/6n7h_0356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7h_0356/09_2025/6n7h_0356.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1035 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 S 88 5.16 5 C 11236 2.51 5 N 2816 2.21 5 O 3099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17242 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7807 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 947} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 7708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7708 Classifications: {'peptide': 988} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 42, 'TRANS': 945} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 4, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1371 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 166} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 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: 8, 154 Unusual residues: {'CLR': 3, 'NAG': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 98 Unusual residues: {'CLR': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {' CA': 2, ' ZN': 1, 'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.49, per 1000 atoms: 0.26 Number of scatterers: 17242 At special positions: 0 Unit cell: (144.82, 93.576, 152.618, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 2 19.99 S 88 16.00 O 3099 8.00 N 2816 7.00 C 11236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 327 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 327 " distance=2.01 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 304 " 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=4, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1801 " - " ASN A 312 " " NAG A1802 " - " ASN A 349 " " NAG A1803 " - " ASN A 414 " " NAG A1804 " - " ASN A 875 " " NAG A1807 " - " ASN A 141 " " NAG B1501 " - " ASN B 141 " " NAG B1502 " - " ASN B 312 " " NAG B1503 " - " ASN B 349 " " NAG B1504 " - " ASN B 414 " " NAG B1505 " - " ASN B 875 " " NAG D 1 " - " ASN A1000 " " NAG E 1 " - " ASN B1000 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 704.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" NE2 HIS C 140 " pdb="ZN ZN C 202 " - pdb=" ND1 HIS C 182 " 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4026 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 10 sheets defined 57.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 74 through 97 removed outlier: 3.672A pdb=" N TRP A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 114 Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.724A pdb=" N LEU A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.513A pdb=" N LEU A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 removed outlier: 3.819A pdb=" N ILE A 219 " --> pdb=" O TYR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.899A pdb=" N ASP A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.519A pdb=" N GLN A 242 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.832A pdb=" N ILE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 388 through 410 Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 438 through 455 Processing helix chain 'A' and resid 467 through 492 removed outlier: 3.850A pdb=" N GLY A 492 " --> pdb=" O CYS A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 503 through 524 removed outlier: 3.769A pdb=" N LEU A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASP A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASP A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 544 removed outlier: 4.391A pdb=" N GLY A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 562 Processing helix chain 'A' and resid 567 through 592 Processing helix chain 'A' and resid 592 through 605 removed outlier: 4.027A pdb=" N ARG A 602 " --> pdb=" O MET A 598 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 605 " --> pdb=" O TYR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 746 Proline residue: A 742 - end of helix Processing helix chain 'A' and resid 750 through 771 removed outlier: 3.603A pdb=" N VAL A 763 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 780 removed outlier: 3.968A pdb=" N ASP A 779 " --> pdb=" O ASP A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 798 removed outlier: 3.543A pdb=" N TYR A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 843 through 864 removed outlier: 3.689A pdb=" N TYR A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU A 864 " --> pdb=" O ASP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 875 removed outlier: 3.616A pdb=" N LYS A 874 " --> pdb=" O ASN A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 888 Processing helix chain 'A' and resid 918 through 930 Processing helix chain 'A' and resid 930 through 937 Processing helix chain 'A' and resid 983 through 1004 removed outlier: 3.648A pdb=" N LEU A1004 " --> pdb=" O ASN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1018 Processing helix chain 'A' and resid 1024 through 1046 removed outlier: 3.971A pdb=" N LEU A1029 " --> pdb=" O ARG A1025 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU A1030 " --> pdb=" O HIS A1026 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1075 removed outlier: 4.165A pdb=" N ILE A1055 " --> pdb=" O TRP A1051 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A1075 " --> pdb=" O MET A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1106 removed outlier: 3.646A pdb=" N VAL A1084 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1122 removed outlier: 3.783A pdb=" N ALA A1115 " --> pdb=" O LYS A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1141 Processing helix chain 'A' and resid 1145 through 1152 removed outlier: 3.917A pdb=" N VAL A1149 " --> pdb=" O PHE A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1178 Proline residue: A1172 - end of helix Processing helix chain 'B' and resid 77 through 97 removed outlier: 3.620A pdb=" N PHE B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 124 through 130 removed outlier: 3.770A pdb=" N LEU B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 removed outlier: 3.750A pdb=" N ARG B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS B 146 " --> pdb=" O TYR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 187 Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 215 through 221 Processing helix chain 'B' and resid 231 through 242 removed outlier: 6.470A pdb=" N TRP B 236 " --> pdb=" O ASP B 233 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLU B 237 " --> pdb=" O CYS B 234 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY B 238 " --> pdb=" O PHE B 235 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN B 242 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 272 removed outlier: 3.556A pdb=" N PHE B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 285 Processing helix chain 'B' and resid 368 through 376 removed outlier: 3.647A pdb=" N PHE B 376 " --> pdb=" O MET B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 409 Processing helix chain 'B' and resid 423 through 435 removed outlier: 4.003A pdb=" N LEU B 427 " --> pdb=" O THR B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 455 Processing helix chain 'B' and resid 467 through 491 removed outlier: 3.621A pdb=" N LEU B 471 " --> pdb=" O GLY B 467 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 removed outlier: 3.922A pdb=" N GLY B 509 " --> pdb=" O PHE B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 524 removed outlier: 3.898A pdb=" N LEU B 518 " --> pdb=" O ASP B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.685A pdb=" N CYS B 540 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 542 " --> pdb=" O GLU B 539 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 543 " --> pdb=" O CYS B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 563 removed outlier: 3.930A pdb=" N ALA B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU B 550 " --> pdb=" O ALA B 546 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 591 Processing helix chain 'B' and resid 592 through 605 removed outlier: 4.304A pdb=" N MET B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 745 removed outlier: 4.319A pdb=" N ALA B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Proline residue: B 742 - end of helix Processing helix chain 'B' and resid 746 through 768 removed outlier: 3.914A pdb=" N VAL B 752 " --> pdb=" O LYS B 748 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 754 " --> pdb=" O LYS B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 798 removed outlier: 3.976A pdb=" N LYS B 796 " --> pdb=" O ALA B 792 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 828 removed outlier: 3.540A pdb=" N TYR B 820 " --> pdb=" O GLN B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 866 removed outlier: 3.981A pdb=" N TYR B 847 " --> pdb=" O MET B 843 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP B 863 " --> pdb=" O PHE B 859 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU B 864 " --> pdb=" O ASP B 860 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR B 865 " --> pdb=" O SER B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 876 removed outlier: 4.271A pdb=" N ASN B 875 " --> pdb=" O ASN B 872 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY B 876 " --> pdb=" O TYR B 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 872 through 876' Processing helix chain 'B' and resid 879 through 889 Processing helix chain 'B' and resid 901 through 906 removed outlier: 4.104A pdb=" N LYS B 904 " --> pdb=" O GLN B 901 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN B 905 " --> pdb=" O LEU B 902 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG B 906 " --> pdb=" O THR B 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 901 through 906' Processing helix chain 'B' and resid 918 through 928 removed outlier: 4.682A pdb=" N THR B 924 " --> pdb=" O TYR B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1004 removed outlier: 3.642A pdb=" N PHE B 987 " --> pdb=" O ASP B 983 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL B 988 " --> pdb=" O THR B 984 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR B1001 " --> pdb=" O ILE B 997 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B1002 " --> pdb=" O CYS B 998 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER B1003 " --> pdb=" O SER B 999 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B1004 " --> pdb=" O ASN B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1016 Processing helix chain 'B' and resid 1018 through 1022 removed outlier: 3.890A pdb=" N TYR B1021 " --> pdb=" O TRP B1018 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B1022 " --> pdb=" O GLU B1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1018 through 1022' Processing helix chain 'B' and resid 1024 through 1046 removed outlier: 4.337A pdb=" N LEU B1030 " --> pdb=" O HIS B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1075 removed outlier: 3.537A pdb=" N GLY B1075 " --> pdb=" O MET B1071 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1106 removed outlier: 4.006A pdb=" N VAL B1083 " --> pdb=" O SER B1079 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B1084 " --> pdb=" O ALA B1080 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B1085 " --> pdb=" O VAL B1081 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B1087 " --> pdb=" O VAL B1083 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N HIS B1099 " --> pdb=" O GLU B1095 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL B1100 " --> pdb=" O PHE B1096 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B1106 " --> pdb=" O LEU B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1138 removed outlier: 3.571A pdb=" N VAL B1116 " --> pdb=" O ASN B1112 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ALA B1124 " --> pdb=" O GLU B1120 " (cutoff:3.500A) Proline residue: B1125 - end of helix Processing helix chain 'B' and resid 1139 through 1143 removed outlier: 3.519A pdb=" N SER B1143 " --> pdb=" O LEU B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1169 removed outlier: 4.494A pdb=" N ILE B1158 " --> pdb=" O ALA B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1169 through 1177 removed outlier: 3.920A pdb=" N VAL B1173 " --> pdb=" O VAL B1169 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.882A pdb=" N ALA C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.863A pdb=" N GLY C 143 " --> pdb=" O HIS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 168 removed outlier: 3.514A pdb=" N ARG C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 229 removed outlier: 3.536A pdb=" N LEU A 360 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 418 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.685A pdb=" N VAL A 347 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 972 through 978 removed outlier: 3.529A pdb=" N ALA A 972 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A1007 " --> pdb=" O GLN A 808 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 908 through 909 removed outlier: 3.568A pdb=" N ASP A 909 " --> pdb=" O ILE A 913 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AA6, first strand: chain 'B' and resid 360 through 361 removed outlier: 3.629A pdb=" N GLN B 160 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE B 422 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 772 through 773 removed outlier: 6.432A pdb=" N ARG B 772 " --> pdb=" O LEU B1078 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 975 through 978 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.206A pdb=" N ILE C 85 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLU C 126 " --> pdb=" O ILE C 85 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASP C 147 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP C 172 " --> pdb=" O SER C 184 " (cutoff:3.500A) 829 hydrogen bonds defined for protein. 2394 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: 3.16 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3608 1.33 - 1.45: 4098 1.45 - 1.57: 9815 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 17665 Sorted by residual: bond pdb=" C MET C 98 " pdb=" N THR C 99 " ideal model delta sigma weight residual 1.332 1.524 -0.192 1.40e-02 5.10e+03 1.87e+02 bond pdb=" C ARG C 123 " pdb=" N VAL C 124 " ideal model delta sigma weight residual 1.330 1.450 -0.120 1.00e-02 1.00e+04 1.43e+02 bond pdb=" C1 NAG B1501 " pdb=" O5 NAG B1501 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" C1 NAG B1504 " pdb=" O5 NAG B1504 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.26e+00 bond pdb=" C PRO A 252 " pdb=" N PRO A 253 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 7.94e+00 ... (remaining 17660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 23133 3.03 - 6.05: 733 6.05 - 9.08: 141 9.08 - 12.10: 26 12.10 - 15.13: 6 Bond angle restraints: 24039 Sorted by residual: angle pdb=" C ASP C 83 " pdb=" N ILE C 84 " pdb=" CA ILE C 84 " ideal model delta sigma weight residual 123.10 136.45 -13.35 1.29e+00 6.01e-01 1.07e+02 angle pdb=" O ASP C 83 " pdb=" C ASP C 83 " pdb=" N ILE C 84 " ideal model delta sigma weight residual 122.19 110.99 11.20 1.21e+00 6.83e-01 8.57e+01 angle pdb=" N GLY C 196 " pdb=" CA GLY C 196 " pdb=" C GLY C 196 " ideal model delta sigma weight residual 115.21 126.82 -11.61 1.30e+00 5.92e-01 7.98e+01 angle pdb=" N ALA C 192 " pdb=" CA ALA C 192 " pdb=" C ALA C 192 " ideal model delta sigma weight residual 108.96 122.19 -13.23 1.59e+00 3.96e-01 6.93e+01 angle pdb=" N ALA C 187 " pdb=" CA ALA C 187 " pdb=" C ALA C 187 " ideal model delta sigma weight residual 112.23 121.09 -8.86 1.26e+00 6.30e-01 4.95e+01 ... (remaining 24034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.86: 10321 23.86 - 47.73: 436 47.73 - 71.59: 50 71.59 - 95.46: 23 95.46 - 119.32: 25 Dihedral angle restraints: 10855 sinusoidal: 4589 harmonic: 6266 Sorted by residual: dihedral pdb=" CA ARG B 942 " pdb=" C ARG B 942 " pdb=" N PRO B 943 " pdb=" CA PRO B 943 " ideal model delta harmonic sigma weight residual 180.00 121.33 58.67 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA ALA B 357 " pdb=" C ALA B 357 " pdb=" N HIS B 358 " pdb=" CA HIS B 358 " ideal model delta harmonic sigma weight residual 180.00 125.07 54.93 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA GLU A 836 " pdb=" C GLU A 836 " pdb=" N ASN A 837 " pdb=" CA ASN A 837 " ideal model delta harmonic sigma weight residual 180.00 -130.59 -49.41 0 5.00e+00 4.00e-02 9.76e+01 ... (remaining 10852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2293 0.089 - 0.178: 422 0.178 - 0.266: 51 0.266 - 0.355: 10 0.355 - 0.444: 4 Chirality restraints: 2780 Sorted by residual: chirality pdb=" C1 NAG B1501 " pdb=" ND2 ASN B 141 " pdb=" C2 NAG B1501 " pdb=" O5 NAG B1501 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" CA ALA C 192 " pdb=" N ALA C 192 " pdb=" C ALA C 192 " pdb=" CB ALA C 192 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C1 NAG A1807 " pdb=" ND2 ASN A 141 " pdb=" C2 NAG A1807 " pdb=" O5 NAG A1807 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 2777 not shown) Planarity restraints: 2996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 83 " 0.032 2.00e-02 2.50e+03 5.73e-02 3.28e+01 pdb=" C ASP C 83 " -0.099 2.00e-02 2.50e+03 pdb=" O ASP C 83 " 0.033 2.00e-02 2.50e+03 pdb=" N ILE C 84 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 123 " -0.025 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C ARG C 123 " 0.082 2.00e-02 2.50e+03 pdb=" O ARG C 123 " -0.031 2.00e-02 2.50e+03 pdb=" N VAL C 124 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A1179 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO A1180 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A1180 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1180 " -0.040 5.00e-02 4.00e+02 ... (remaining 2993 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 152 2.59 - 3.16: 14447 3.16 - 3.74: 26536 3.74 - 4.32: 34992 4.32 - 4.90: 57183 Nonbonded interactions: 133310 Sorted by model distance: nonbonded pdb=" O ALA C 187 " pdb=" N ASN C 189 " model vdw 2.008 3.120 nonbonded pdb=" OD2 ASP C 147 " pdb="ZN ZN C 202 " model vdw 2.125 2.230 nonbonded pdb=" OE1 GLU B 149 " pdb=" NH2 ARG C 28 " model vdw 2.159 3.120 nonbonded pdb=" OD1 ASP C 147 " pdb="ZN ZN C 202 " model vdw 2.225 2.230 nonbonded pdb=" OD2 ASP B 821 " pdb=" OH TYR B1001 " model vdw 2.242 3.040 ... (remaining 133305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 76 through 458 or (resid 459 through 466 and (name N or na \ me CA or name C or name O or name CB )) or resid 467 through 606 or resid 731 th \ rough 888 or (resid 889 and (name N or name CA or name C or name O or name CB )) \ or resid 890 through 892 or (resid 893 through 905 and (name N or name CA or na \ me C or name O or name CB )) or resid 906 through 953 or (resid 954 through 959 \ and (name N or name CA or name C or name O or name CB )) or resid 960 or (resid \ 961 and (name N or name CA or name C or name O or name CB )) or resid 962 throug \ h 1182 or (resid 1183 and (name N or name CA or name C or name O or name CB )) o \ r resid 1803 through 1807 or resid 1810)) selection = (chain 'B' and (resid 76 through 606 or (resid 731 through 737 and (name N or na \ me CA or name C or name O or name CB )) or resid 738 through 1503 or resid 1508) \ ) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.730 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 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 : 0.011 0.440 17691 Z= 0.615 Angle : 1.333 15.126 24093 Z= 0.676 Chirality : 0.071 0.444 2780 Planarity : 0.009 0.073 2984 Dihedral : 14.944 119.321 6811 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.32 % Favored : 87.12 % Rotamer: Outliers : 1.35 % Allowed : 8.53 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.46 (0.14), residues: 2143 helix: -2.49 (0.11), residues: 1142 sheet: -3.32 (0.40), residues: 115 loop : -3.44 (0.18), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 945 TYR 0.033 0.004 TYR A1181 PHE 0.040 0.004 PHE B1152 TRP 0.040 0.004 TRP B 399 HIS 0.014 0.003 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00953 (17665) covalent geometry : angle 1.31594 (24039) SS BOND : bond 0.00872 ( 6) SS BOND : angle 2.80429 ( 12) hydrogen bonds : bond 0.16146 ( 829) hydrogen bonds : angle 6.84799 ( 2394) metal coordination : bond 0.15262 ( 2) Misc. bond : bond 0.28808 ( 4) link_BETA1-4 : bond 0.00549 ( 2) link_BETA1-4 : angle 3.06033 ( 6) link_NAG-ASN : bond 0.01334 ( 12) link_NAG-ASN : angle 5.37018 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 529 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8375 (pp) cc_final: 0.8072 (mt) REVERT: A 131 GLU cc_start: 0.8146 (tt0) cc_final: 0.7786 (tt0) REVERT: A 420 LEU cc_start: 0.7393 (pt) cc_final: 0.5636 (mt) REVERT: A 464 LYS cc_start: 0.7334 (mmtm) cc_final: 0.6720 (ttpt) REVERT: A 501 GLN cc_start: 0.7156 (mt0) cc_final: 0.6816 (tp-100) REVERT: A 550 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8784 (tm) REVERT: A 599 ASP cc_start: 0.7511 (t0) cc_final: 0.7099 (t70) REVERT: A 791 ILE cc_start: 0.9317 (mm) cc_final: 0.9088 (mt) REVERT: A 799 SER cc_start: 0.8475 (p) cc_final: 0.8264 (p) REVERT: A 850 ASP cc_start: 0.8118 (t0) cc_final: 0.7797 (t0) REVERT: A 870 PRO cc_start: 0.6715 (Cg_endo) cc_final: 0.5552 (Cg_exo) REVERT: A 956 MET cc_start: 0.8437 (ptt) cc_final: 0.8178 (ptt) REVERT: A 1013 TYR cc_start: 0.7886 (m-10) cc_final: 0.7600 (m-80) REVERT: A 1052 THR cc_start: 0.8108 (p) cc_final: 0.7890 (t) REVERT: A 1063 MET cc_start: 0.7481 (tpt) cc_final: 0.7186 (ttt) REVERT: A 1073 LEU cc_start: 0.8536 (mt) cc_final: 0.8073 (tp) REVERT: B 82 LYS cc_start: 0.6921 (tptm) cc_final: 0.6515 (mttt) REVERT: B 88 PHE cc_start: 0.5523 (t80) cc_final: 0.4974 (t80) REVERT: B 210 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6081 (pp) REVERT: B 216 MET cc_start: 0.7841 (tpp) cc_final: 0.7373 (tpp) REVERT: B 354 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7428 (pp) REVERT: B 430 ILE cc_start: 0.8488 (tp) cc_final: 0.8259 (pt) REVERT: B 487 LEU cc_start: 0.8198 (tp) cc_final: 0.7760 (tp) REVERT: B 606 ARG cc_start: 0.5980 (mtm180) cc_final: 0.5611 (mtt-85) REVERT: B 744 LEU cc_start: 0.6111 (tt) cc_final: 0.5730 (mt) REVERT: B 760 LEU cc_start: 0.6622 (tt) cc_final: 0.6096 (mm) REVERT: B 868 ILE cc_start: 0.6324 (OUTLIER) cc_final: 0.5838 (tp) REVERT: B 962 ARG cc_start: 0.7181 (ttt180) cc_final: 0.6651 (tpp80) REVERT: B 1040 PHE cc_start: 0.7792 (t80) cc_final: 0.7518 (t80) REVERT: B 1099 HIS cc_start: 0.7146 (m-70) cc_final: 0.6927 (m-70) REVERT: B 1119 LEU cc_start: 0.7999 (tp) cc_final: 0.7418 (tp) REVERT: C 72 ARG cc_start: 0.6754 (mtp-110) cc_final: 0.6409 (mtp180) REVERT: C 114 MET cc_start: 0.8318 (mtm) cc_final: 0.8099 (mtp) REVERT: C 183 CYS cc_start: 0.7974 (m) cc_final: 0.7743 (m) outliers start: 24 outliers final: 7 residues processed: 545 average time/residue: 0.1540 time to fit residues: 123.8562 Evaluate side-chains 285 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 274 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 1171 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 188 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 0.0270 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 97 ASN A 156 GLN A 184 GLN A 310 ASN A 496 ASN A 823 HIS A 871 ASN A 929 ASN A1049 ASN B 120 ASN B 124 ASN B 156 GLN B 201 HIS B 242 GLN B 310 ASN ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 846 HIS B 853 GLN ** B 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 929 ASN B 938 GLN B1049 ASN C 69 ASN C 107 ASN C 134 HIS C 180 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.143199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.121176 restraints weight = 29633.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123560 restraints weight = 18282.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124495 restraints weight = 12761.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.124607 restraints weight = 10703.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.125838 restraints weight = 10318.105| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17691 Z= 0.154 Angle : 0.832 16.107 24093 Z= 0.403 Chirality : 0.049 0.414 2780 Planarity : 0.006 0.063 2984 Dihedral : 11.471 74.303 2983 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.75 % Favored : 90.11 % Rotamer: Outliers : 4.21 % Allowed : 13.92 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.17), residues: 2143 helix: -0.86 (0.14), residues: 1161 sheet: -2.33 (0.43), residues: 114 loop : -2.99 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 138 TYR 0.026 0.002 TYR A 224 PHE 0.020 0.002 PHE A 848 TRP 0.026 0.002 TRP A1027 HIS 0.010 0.001 HIS B 739 Details of bonding type rmsd covalent geometry : bond 0.00321 (17665) covalent geometry : angle 0.81585 (24039) SS BOND : bond 0.01332 ( 6) SS BOND : angle 2.42681 ( 12) hydrogen bonds : bond 0.04680 ( 829) hydrogen bonds : angle 4.97985 ( 2394) metal coordination : bond 0.00628 ( 2) Misc. bond : bond 0.00225 ( 4) link_BETA1-4 : bond 0.00392 ( 2) link_BETA1-4 : angle 1.53667 ( 6) link_NAG-ASN : bond 0.00570 ( 12) link_NAG-ASN : angle 4.07767 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 323 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8487 (pp) cc_final: 0.8264 (mt) REVERT: A 173 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7546 (pt0) REVERT: A 292 MET cc_start: 0.7963 (mmt) cc_final: 0.7604 (mmt) REVERT: A 434 PHE cc_start: 0.7100 (t80) cc_final: 0.6864 (t80) REVERT: A 464 LYS cc_start: 0.7308 (mmtm) cc_final: 0.6673 (ttpt) REVERT: A 862 ASP cc_start: 0.7165 (t70) cc_final: 0.6853 (t0) REVERT: A 1051 TRP cc_start: 0.6895 (t-100) cc_final: 0.6301 (t60) REVERT: A 1073 LEU cc_start: 0.8328 (mt) cc_final: 0.8086 (tp) REVERT: A 1175 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8903 (mt) REVERT: B 82 LYS cc_start: 0.6974 (tptm) cc_final: 0.6549 (mptt) REVERT: B 101 PHE cc_start: 0.6131 (OUTLIER) cc_final: 0.5711 (t80) REVERT: B 102 LEU cc_start: 0.5478 (mp) cc_final: 0.5207 (tt) REVERT: B 210 ILE cc_start: 0.6474 (OUTLIER) cc_final: 0.5911 (pp) REVERT: B 354 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7434 (pp) REVERT: B 430 ILE cc_start: 0.8333 (tp) cc_final: 0.8082 (pt) REVERT: B 606 ARG cc_start: 0.5939 (mtm180) cc_final: 0.5621 (mtt-85) REVERT: B 760 LEU cc_start: 0.6536 (tt) cc_final: 0.5848 (mm) REVERT: B 821 ASP cc_start: 0.6751 (m-30) cc_final: 0.6542 (m-30) REVERT: B 868 ILE cc_start: 0.6216 (OUTLIER) cc_final: 0.5878 (tp) REVERT: B 962 ARG cc_start: 0.7049 (ttt180) cc_final: 0.6791 (tpp80) REVERT: B 1040 PHE cc_start: 0.7674 (t80) cc_final: 0.7428 (t80) outliers start: 75 outliers final: 24 residues processed: 375 average time/residue: 0.1325 time to fit residues: 77.1616 Evaluate side-chains 273 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 944 HIS Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 129 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 148 optimal weight: 0.0060 chunk 193 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 103 optimal weight: 0.0770 chunk 80 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 204 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 901 GLN ** A1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS B 375 HIS ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 823 HIS ** B 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.142708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120610 restraints weight = 29748.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.123197 restraints weight = 18272.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124073 restraints weight = 12477.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.124503 restraints weight = 10728.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.124704 restraints weight = 9959.227| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17691 Z= 0.136 Angle : 0.775 13.972 24093 Z= 0.374 Chirality : 0.047 0.482 2780 Planarity : 0.005 0.075 2984 Dihedral : 9.229 58.173 2976 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 3.87 % Allowed : 16.67 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.17), residues: 2143 helix: -0.13 (0.15), residues: 1174 sheet: -1.87 (0.44), residues: 119 loop : -2.84 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1113 TYR 0.037 0.002 TYR A1001 PHE 0.019 0.001 PHE B 88 TRP 0.024 0.001 TRP A1027 HIS 0.006 0.001 HIS B 739 Details of bonding type rmsd covalent geometry : bond 0.00284 (17665) covalent geometry : angle 0.76146 (24039) SS BOND : bond 0.00266 ( 6) SS BOND : angle 1.94178 ( 12) hydrogen bonds : bond 0.04154 ( 829) hydrogen bonds : angle 4.64403 ( 2394) metal coordination : bond 0.00192 ( 2) Misc. bond : bond 0.00092 ( 4) link_BETA1-4 : bond 0.00424 ( 2) link_BETA1-4 : angle 1.24049 ( 6) link_NAG-ASN : bond 0.00672 ( 12) link_NAG-ASN : angle 3.67853 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 278 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8354 (pp) cc_final: 0.8146 (mt) REVERT: A 173 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7544 (pt0) REVERT: A 422 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6517 (p90) REVERT: A 434 PHE cc_start: 0.6955 (t80) cc_final: 0.6697 (t80) REVERT: A 447 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6963 (tp) REVERT: A 464 LYS cc_start: 0.7357 (mmtm) cc_final: 0.6696 (ttmt) REVERT: A 783 ARG cc_start: 0.7527 (mtp-110) cc_final: 0.7301 (mtp-110) REVERT: A 821 ASP cc_start: 0.7122 (t70) cc_final: 0.6779 (t0) REVERT: A 843 MET cc_start: 0.8391 (ttp) cc_final: 0.8110 (ttm) REVERT: A 862 ASP cc_start: 0.7273 (t70) cc_final: 0.6999 (t0) REVERT: A 1051 TRP cc_start: 0.7056 (t-100) cc_final: 0.6318 (t60) REVERT: A 1122 MET cc_start: 0.7906 (ttm) cc_final: 0.7352 (ttm) REVERT: A 1175 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8926 (mt) REVERT: B 82 LYS cc_start: 0.7042 (tptm) cc_final: 0.6588 (mptt) REVERT: B 101 PHE cc_start: 0.6487 (OUTLIER) cc_final: 0.6117 (t80) REVERT: B 140 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8423 (mp) REVERT: B 157 LEU cc_start: 0.9049 (mp) cc_final: 0.8785 (mt) REVERT: B 210 ILE cc_start: 0.6532 (OUTLIER) cc_final: 0.6023 (pp) REVERT: B 354 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7375 (pp) REVERT: B 429 ASP cc_start: 0.7403 (t0) cc_final: 0.7007 (t0) REVERT: B 430 ILE cc_start: 0.8350 (tp) cc_final: 0.8063 (pt) REVERT: B 606 ARG cc_start: 0.5825 (mtm180) cc_final: 0.5497 (mtt-85) REVERT: B 760 LEU cc_start: 0.6296 (tt) cc_final: 0.5566 (mm) REVERT: B 821 ASP cc_start: 0.6726 (m-30) cc_final: 0.6525 (m-30) REVERT: B 1040 PHE cc_start: 0.7601 (t80) cc_final: 0.7358 (t80) REVERT: B 1123 PHE cc_start: 0.8069 (t80) cc_final: 0.7427 (t80) REVERT: C 129 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7878 (p0) outliers start: 69 outliers final: 34 residues processed: 324 average time/residue: 0.1288 time to fit residues: 65.9577 Evaluate side-chains 280 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 944 HIS Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1177 PHE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 129 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 GLN A 846 HIS A 901 GLN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 375 HIS ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 872 ASN ** B 929 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 = 0.3743 r_free = 0.3743 target = 0.134868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112819 restraints weight = 29945.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114963 restraints weight = 18857.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.116137 restraints weight = 13604.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.116220 restraints weight = 11499.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116303 restraints weight = 10633.745| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17691 Z= 0.210 Angle : 0.818 13.396 24093 Z= 0.401 Chirality : 0.050 0.548 2780 Planarity : 0.006 0.085 2984 Dihedral : 8.357 56.728 2974 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.97 % Favored : 88.94 % Rotamer: Outliers : 5.27 % Allowed : 17.62 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.18), residues: 2143 helix: 0.23 (0.15), residues: 1172 sheet: -1.59 (0.46), residues: 121 loop : -2.77 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1114 TYR 0.031 0.002 TYR A 224 PHE 0.027 0.002 PHE A 848 TRP 0.017 0.002 TRP A 278 HIS 0.007 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00483 (17665) covalent geometry : angle 0.80183 (24039) SS BOND : bond 0.00450 ( 6) SS BOND : angle 2.57737 ( 12) hydrogen bonds : bond 0.04621 ( 829) hydrogen bonds : angle 4.59842 ( 2394) metal coordination : bond 0.00479 ( 2) Misc. bond : bond 0.00059 ( 4) link_BETA1-4 : bond 0.00818 ( 2) link_BETA1-4 : angle 1.55555 ( 6) link_NAG-ASN : bond 0.00794 ( 12) link_NAG-ASN : angle 4.01292 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 252 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8455 (pp) cc_final: 0.8148 (mt) REVERT: A 276 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6958 (p0) REVERT: A 315 LYS cc_start: 0.6505 (pptt) cc_final: 0.6178 (tptp) REVERT: A 417 GLN cc_start: 0.6944 (mm-40) cc_final: 0.6735 (mm-40) REVERT: A 422 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.6729 (p90) REVERT: A 447 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7245 (tp) REVERT: A 575 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8169 (mt) REVERT: A 843 MET cc_start: 0.8539 (ttp) cc_final: 0.8281 (ttm) REVERT: A 856 GLN cc_start: 0.6232 (tm-30) cc_final: 0.5965 (tm-30) REVERT: A 862 ASP cc_start: 0.7465 (t70) cc_final: 0.7143 (t0) REVERT: A 956 MET cc_start: 0.8359 (ptt) cc_final: 0.7988 (ptt) REVERT: A 1051 TRP cc_start: 0.7321 (t-100) cc_final: 0.6381 (t60) REVERT: A 1175 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8737 (mt) REVERT: B 85 ARG cc_start: 0.7267 (tpt-90) cc_final: 0.5357 (tmm-80) REVERT: B 101 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.6331 (t80) REVERT: B 136 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8581 (t) REVERT: B 140 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8462 (mp) REVERT: B 210 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6314 (pp) REVERT: B 429 ASP cc_start: 0.7393 (t0) cc_final: 0.7139 (t0) REVERT: B 430 ILE cc_start: 0.8280 (tp) cc_final: 0.7969 (pt) REVERT: B 606 ARG cc_start: 0.5762 (mtm180) cc_final: 0.5402 (mtt-85) REVERT: B 760 LEU cc_start: 0.6525 (tt) cc_final: 0.5904 (mm) REVERT: B 821 ASP cc_start: 0.6985 (m-30) cc_final: 0.6755 (m-30) REVERT: C 67 SER cc_start: 0.8344 (p) cc_final: 0.8031 (m) outliers start: 94 outliers final: 54 residues processed: 325 average time/residue: 0.1285 time to fit residues: 65.8414 Evaluate side-chains 291 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 228 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 944 HIS Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1056 ILE Chi-restraints excluded: chain B residue 1059 VAL Chi-restraints excluded: chain B residue 1108 ILE Chi-restraints excluded: chain B residue 1165 LEU Chi-restraints excluded: chain B residue 1177 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 129 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 166 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 187 optimal weight: 0.1980 chunk 87 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 0.0020 chunk 213 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS B 196 GLN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114739 restraints weight = 29519.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.117582 restraints weight = 18056.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118413 restraints weight = 12092.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.118685 restraints weight = 10681.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.118733 restraints weight = 10012.030| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17691 Z= 0.148 Angle : 0.756 11.666 24093 Z= 0.367 Chirality : 0.047 0.482 2780 Planarity : 0.005 0.072 2984 Dihedral : 7.997 56.945 2974 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 4.49 % Allowed : 19.36 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.18), residues: 2143 helix: 0.54 (0.15), residues: 1175 sheet: -1.21 (0.49), residues: 119 loop : -2.70 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 893 TYR 0.028 0.001 TYR A 224 PHE 0.020 0.001 PHE B1040 TRP 0.017 0.001 TRP A1027 HIS 0.007 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00329 (17665) covalent geometry : angle 0.73983 (24039) SS BOND : bond 0.00300 ( 6) SS BOND : angle 2.80502 ( 12) hydrogen bonds : bond 0.04097 ( 829) hydrogen bonds : angle 4.41718 ( 2394) metal coordination : bond 0.00292 ( 2) Misc. bond : bond 0.00063 ( 4) link_BETA1-4 : bond 0.00356 ( 2) link_BETA1-4 : angle 1.32424 ( 6) link_NAG-ASN : bond 0.00647 ( 12) link_NAG-ASN : angle 3.75602 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 251 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7426 (pt0) REVERT: A 179 LEU cc_start: 0.8906 (tp) cc_final: 0.8697 (tt) REVERT: A 276 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6944 (p0) REVERT: A 422 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6481 (p90) REVERT: A 447 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7244 (tp) REVERT: A 455 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6615 (mm) REVERT: A 862 ASP cc_start: 0.7325 (t70) cc_final: 0.7085 (t0) REVERT: A 956 MET cc_start: 0.8428 (ptt) cc_final: 0.8004 (ptt) REVERT: A 1051 TRP cc_start: 0.7222 (t-100) cc_final: 0.6358 (t60) REVERT: A 1175 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8782 (mt) REVERT: B 85 ARG cc_start: 0.7269 (tpt-90) cc_final: 0.5379 (tmm-80) REVERT: B 101 PHE cc_start: 0.6772 (OUTLIER) cc_final: 0.6346 (t80) REVERT: B 136 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8565 (t) REVERT: B 140 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8471 (mp) REVERT: B 210 ILE cc_start: 0.6874 (OUTLIER) cc_final: 0.6449 (pp) REVERT: B 429 ASP cc_start: 0.7379 (t0) cc_final: 0.7161 (t0) REVERT: B 430 ILE cc_start: 0.8183 (tp) cc_final: 0.7872 (pt) REVERT: B 739 HIS cc_start: 0.3347 (t-90) cc_final: 0.3100 (t-170) REVERT: B 1027 TRP cc_start: 0.6537 (m-10) cc_final: 0.6329 (m-10) REVERT: C 67 SER cc_start: 0.8311 (p) cc_final: 0.8019 (m) outliers start: 80 outliers final: 47 residues processed: 305 average time/residue: 0.1265 time to fit residues: 61.5788 Evaluate side-chains 282 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 225 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 944 HIS Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1177 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 129 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 168 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 201 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1112 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116932 restraints weight = 29644.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119726 restraints weight = 17783.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.120897 restraints weight = 12034.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121059 restraints weight = 10555.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121143 restraints weight = 10102.838| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17691 Z= 0.128 Angle : 0.734 14.988 24093 Z= 0.352 Chirality : 0.045 0.425 2780 Planarity : 0.005 0.071 2984 Dihedral : 7.642 57.004 2974 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 4.15 % Allowed : 20.99 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.19), residues: 2143 helix: 0.88 (0.16), residues: 1159 sheet: -0.98 (0.49), residues: 119 loop : -2.54 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1114 TYR 0.028 0.001 TYR A 224 PHE 0.025 0.001 PHE B 88 TRP 0.018 0.001 TRP A1027 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00274 (17665) covalent geometry : angle 0.71940 (24039) SS BOND : bond 0.00318 ( 6) SS BOND : angle 1.99084 ( 12) hydrogen bonds : bond 0.03725 ( 829) hydrogen bonds : angle 4.24084 ( 2394) metal coordination : bond 0.00135 ( 2) Misc. bond : bond 0.00056 ( 4) link_BETA1-4 : bond 0.00395 ( 2) link_BETA1-4 : angle 1.22597 ( 6) link_NAG-ASN : bond 0.00695 ( 12) link_NAG-ASN : angle 3.62267 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 259 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7892 (mt) REVERT: A 173 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7355 (pt0) REVERT: A 179 LEU cc_start: 0.8966 (tp) cc_final: 0.8757 (tt) REVERT: A 315 LYS cc_start: 0.6614 (pptt) cc_final: 0.6245 (tptp) REVERT: A 422 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6419 (p90) REVERT: A 447 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.7025 (tp) REVERT: A 956 MET cc_start: 0.8454 (ptt) cc_final: 0.8054 (ptt) REVERT: A 1020 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7295 (pt0) REVERT: A 1051 TRP cc_start: 0.7298 (t-100) cc_final: 0.6374 (t60) REVERT: A 1175 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8775 (mt) REVERT: B 85 ARG cc_start: 0.7277 (tpt-90) cc_final: 0.7063 (tpt-90) REVERT: B 101 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.6382 (t80) REVERT: B 140 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8401 (mp) REVERT: B 210 ILE cc_start: 0.6975 (OUTLIER) cc_final: 0.6594 (pp) REVERT: B 361 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7510 (tp40) REVERT: B 429 ASP cc_start: 0.7360 (t0) cc_final: 0.7126 (t0) REVERT: B 430 ILE cc_start: 0.8220 (tp) cc_final: 0.7931 (pt) REVERT: B 449 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7703 (mmm) REVERT: B 457 MET cc_start: 0.4363 (mpt) cc_final: 0.4100 (mpp) REVERT: B 748 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.5904 (mttt) REVERT: B 761 LEU cc_start: 0.8073 (tt) cc_final: 0.7836 (tt) REVERT: B 1042 VAL cc_start: 0.8432 (t) cc_final: 0.8205 (p) REVERT: C 67 SER cc_start: 0.8312 (p) cc_final: 0.8037 (m) outliers start: 74 outliers final: 48 residues processed: 312 average time/residue: 0.1259 time to fit residues: 62.4219 Evaluate side-chains 289 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 229 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 944 HIS Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1056 ILE Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1177 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 129 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 75 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114626 restraints weight = 29691.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117401 restraints weight = 18093.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118577 restraints weight = 12278.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118602 restraints weight = 10718.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.118794 restraints weight = 10307.877| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17691 Z= 0.149 Angle : 0.742 13.493 24093 Z= 0.360 Chirality : 0.046 0.458 2780 Planarity : 0.005 0.068 2984 Dihedral : 7.643 59.749 2974 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 4.60 % Allowed : 21.04 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.19), residues: 2143 helix: 0.95 (0.16), residues: 1157 sheet: -1.06 (0.48), residues: 119 loop : -2.43 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 401 TYR 0.026 0.001 TYR A 224 PHE 0.017 0.001 PHE A 790 TRP 0.025 0.001 TRP A 278 HIS 0.008 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00335 (17665) covalent geometry : angle 0.72868 (24039) SS BOND : bond 0.00306 ( 6) SS BOND : angle 2.02856 ( 12) hydrogen bonds : bond 0.03839 ( 829) hydrogen bonds : angle 4.21911 ( 2394) metal coordination : bond 0.00342 ( 2) Misc. bond : bond 0.00235 ( 4) link_BETA1-4 : bond 0.00336 ( 2) link_BETA1-4 : angle 1.28817 ( 6) link_NAG-ASN : bond 0.00606 ( 12) link_NAG-ASN : angle 3.54073 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 237 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7373 (pt0) REVERT: A 179 LEU cc_start: 0.8917 (tp) cc_final: 0.8674 (tt) REVERT: A 315 LYS cc_start: 0.6685 (pptt) cc_final: 0.6269 (tptp) REVERT: A 422 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6403 (p90) REVERT: A 447 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7126 (tp) REVERT: A 455 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6319 (mm) REVERT: A 956 MET cc_start: 0.8517 (ptt) cc_final: 0.8142 (ptt) REVERT: A 1020 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7284 (pt0) REVERT: A 1051 TRP cc_start: 0.7318 (t-100) cc_final: 0.6413 (t60) REVERT: A 1063 MET cc_start: 0.7065 (mmm) cc_final: 0.6684 (mmm) REVERT: A 1175 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8800 (mt) REVERT: B 101 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.6195 (t80) REVERT: B 140 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8524 (mp) REVERT: B 210 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6645 (pt) REVERT: B 227 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8464 (tt) REVERT: B 268 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8160 (tt) REVERT: B 361 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7428 (tp40) REVERT: B 429 ASP cc_start: 0.7400 (t0) cc_final: 0.7137 (t0) REVERT: B 430 ILE cc_start: 0.8224 (tp) cc_final: 0.7929 (pt) REVERT: B 449 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7720 (mmm) REVERT: B 748 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.5916 (mttt) REVERT: B 761 LEU cc_start: 0.8035 (tt) cc_final: 0.7770 (tt) REVERT: C 67 SER cc_start: 0.8351 (p) cc_final: 0.8111 (m) outliers start: 82 outliers final: 59 residues processed: 295 average time/residue: 0.1223 time to fit residues: 58.0375 Evaluate side-chains 300 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 227 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 944 HIS Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1056 ILE Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1108 ILE Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1177 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 129 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 27 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS ** B 929 ASN ** 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 = 0.3787 r_free = 0.3787 target = 0.138566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.116218 restraints weight = 29830.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.119259 restraints weight = 18115.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119860 restraints weight = 12290.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.120087 restraints weight = 10967.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.120328 restraints weight = 10742.041| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17691 Z= 0.130 Angle : 0.726 13.136 24093 Z= 0.351 Chirality : 0.045 0.422 2780 Planarity : 0.005 0.065 2984 Dihedral : 7.543 56.784 2974 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 4.43 % Allowed : 21.44 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.19), residues: 2143 helix: 1.03 (0.16), residues: 1161 sheet: -1.07 (0.49), residues: 121 loop : -2.37 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1114 TYR 0.028 0.001 TYR A 224 PHE 0.027 0.001 PHE B 88 TRP 0.028 0.001 TRP A 278 HIS 0.007 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00283 (17665) covalent geometry : angle 0.71380 (24039) SS BOND : bond 0.00261 ( 6) SS BOND : angle 1.80608 ( 12) hydrogen bonds : bond 0.03593 ( 829) hydrogen bonds : angle 4.11458 ( 2394) metal coordination : bond 0.00218 ( 2) Misc. bond : bond 0.00183 ( 4) link_BETA1-4 : bond 0.00433 ( 2) link_BETA1-4 : angle 1.22338 ( 6) link_NAG-ASN : bond 0.00731 ( 12) link_NAG-ASN : angle 3.39185 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 241 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7358 (pt0) REVERT: A 179 LEU cc_start: 0.9013 (tp) cc_final: 0.8793 (tt) REVERT: A 315 LYS cc_start: 0.6597 (pptt) cc_final: 0.6314 (tptp) REVERT: A 422 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6377 (p90) REVERT: A 447 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7124 (tp) REVERT: A 956 MET cc_start: 0.8497 (ptt) cc_final: 0.8194 (ptt) REVERT: A 1020 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7266 (pt0) REVERT: A 1051 TRP cc_start: 0.7330 (t-100) cc_final: 0.6422 (t60) REVERT: A 1175 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8850 (mt) REVERT: B 101 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.6175 (t80) REVERT: B 140 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8391 (mp) REVERT: B 210 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6530 (pt) REVERT: B 227 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8423 (tt) REVERT: B 268 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8170 (tt) REVERT: B 361 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7367 (tp40) REVERT: B 430 ILE cc_start: 0.8233 (tp) cc_final: 0.7923 (pt) REVERT: B 449 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7648 (mmm) REVERT: B 748 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.5941 (mtmt) REVERT: B 761 LEU cc_start: 0.7940 (tt) cc_final: 0.7716 (tt) REVERT: B 1020 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7609 (pp30) REVERT: C 111 ILE cc_start: 0.8676 (mm) cc_final: 0.8353 (mt) outliers start: 79 outliers final: 56 residues processed: 296 average time/residue: 0.1235 time to fit residues: 58.4695 Evaluate side-chains 298 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 228 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 944 HIS Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1059 VAL Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1177 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 122 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 175 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS ** B 929 ASN ** 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 = 0.3779 r_free = 0.3779 target = 0.137764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114997 restraints weight = 29618.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118194 restraints weight = 17824.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119406 restraints weight = 11678.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.119615 restraints weight = 10246.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.119606 restraints weight = 9943.189| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17691 Z= 0.141 Angle : 0.738 12.677 24093 Z= 0.357 Chirality : 0.045 0.414 2780 Planarity : 0.005 0.091 2984 Dihedral : 7.438 59.962 2972 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 4.26 % Allowed : 22.28 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.19), residues: 2143 helix: 1.06 (0.16), residues: 1161 sheet: -1.06 (0.49), residues: 121 loop : -2.36 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 960 TYR 0.027 0.001 TYR A 224 PHE 0.015 0.001 PHE A 522 TRP 0.024 0.001 TRP A 278 HIS 0.010 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00321 (17665) covalent geometry : angle 0.72463 (24039) SS BOND : bond 0.00313 ( 6) SS BOND : angle 2.26236 ( 12) hydrogen bonds : bond 0.03684 ( 829) hydrogen bonds : angle 4.11414 ( 2394) metal coordination : bond 0.00290 ( 2) Misc. bond : bond 0.00120 ( 4) link_BETA1-4 : bond 0.00316 ( 2) link_BETA1-4 : angle 1.20998 ( 6) link_NAG-ASN : bond 0.00645 ( 12) link_NAG-ASN : angle 3.39919 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 245 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: A 315 LYS cc_start: 0.6727 (pptt) cc_final: 0.6351 (tptp) REVERT: A 422 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.6552 (p90) REVERT: A 447 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7115 (tp) REVERT: A 956 MET cc_start: 0.8616 (ptt) cc_final: 0.8203 (ptt) REVERT: A 1020 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7303 (pt0) REVERT: A 1051 TRP cc_start: 0.7390 (t-100) cc_final: 0.6423 (t60) REVERT: A 1175 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8872 (mt) REVERT: B 101 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.6030 (t80) REVERT: B 140 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8322 (mp) REVERT: B 210 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6505 (pt) REVERT: B 227 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8436 (tt) REVERT: B 268 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8118 (tt) REVERT: B 361 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: B 430 ILE cc_start: 0.8226 (tp) cc_final: 0.7916 (pt) REVERT: B 457 MET cc_start: 0.5452 (mpp) cc_final: 0.5171 (mpp) REVERT: B 748 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6023 (mttt) REVERT: B 761 LEU cc_start: 0.7973 (tt) cc_final: 0.7728 (tt) REVERT: B 1020 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7589 (pp30) REVERT: C 83 ASP cc_start: 0.8626 (m-30) cc_final: 0.8394 (t0) outliers start: 76 outliers final: 59 residues processed: 301 average time/residue: 0.1278 time to fit residues: 60.8976 Evaluate side-chains 312 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 240 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 944 HIS Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1059 VAL Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1177 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 167 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 202 optimal weight: 0.5980 chunk 190 optimal weight: 0.1980 chunk 124 optimal weight: 0.0980 chunk 27 optimal weight: 4.9990 chunk 203 optimal weight: 0.6980 chunk 205 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 905 GLN A1020 GLN A1112 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN B 388 ASN B 739 HIS ** B 929 ASN ** 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 = 0.3812 r_free = 0.3812 target = 0.140557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.117568 restraints weight = 29444.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120616 restraints weight = 17967.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121815 restraints weight = 11954.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121987 restraints weight = 10629.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122252 restraints weight = 10069.104| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17691 Z= 0.124 Angle : 0.733 12.664 24093 Z= 0.351 Chirality : 0.044 0.426 2780 Planarity : 0.005 0.082 2984 Dihedral : 7.122 56.899 2972 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.37 % Allowed : 23.29 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.19), residues: 2143 helix: 1.15 (0.16), residues: 1168 sheet: -0.97 (0.49), residues: 121 loop : -2.29 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 960 TYR 0.027 0.001 TYR A 224 PHE 0.024 0.001 PHE B 88 TRP 0.022 0.001 TRP A 278 HIS 0.011 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00267 (17665) covalent geometry : angle 0.72074 (24039) SS BOND : bond 0.00800 ( 6) SS BOND : angle 1.76796 ( 12) hydrogen bonds : bond 0.03398 ( 829) hydrogen bonds : angle 4.01918 ( 2394) metal coordination : bond 0.00115 ( 2) Misc. bond : bond 0.00097 ( 4) link_BETA1-4 : bond 0.00481 ( 2) link_BETA1-4 : angle 1.21553 ( 6) link_NAG-ASN : bond 0.00714 ( 12) link_NAG-ASN : angle 3.34155 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 255 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.5452 (mm-30) cc_final: 0.5203 (mm-30) REVERT: A 173 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7414 (pt0) REVERT: A 315 LYS cc_start: 0.6668 (pptt) cc_final: 0.6448 (tptp) REVERT: A 379 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.8287 (m-80) REVERT: A 422 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.6743 (p90) REVERT: A 447 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7062 (tp) REVERT: A 956 MET cc_start: 0.8621 (ptt) cc_final: 0.8229 (ptt) REVERT: A 1051 TRP cc_start: 0.7421 (t-100) cc_final: 0.6435 (t60) REVERT: A 1175 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8841 (mt) REVERT: B 101 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.6024 (t80) REVERT: B 140 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8082 (mp) REVERT: B 164 GLU cc_start: 0.6432 (tm-30) cc_final: 0.5943 (tm-30) REVERT: B 210 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6329 (pt) REVERT: B 227 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8393 (tt) REVERT: B 268 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8095 (tt) REVERT: B 361 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7405 (tp40) REVERT: B 430 ILE cc_start: 0.8169 (tp) cc_final: 0.7886 (pt) REVERT: B 457 MET cc_start: 0.4982 (mpp) cc_final: 0.4748 (mpp) REVERT: B 522 PHE cc_start: 0.7553 (t80) cc_final: 0.7253 (t80) REVERT: B 748 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.5990 (mtmt) REVERT: B 761 LEU cc_start: 0.7829 (tt) cc_final: 0.7622 (tt) REVERT: B 1020 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7611 (pp30) REVERT: C 83 ASP cc_start: 0.8609 (m-30) cc_final: 0.8406 (t0) REVERT: C 111 ILE cc_start: 0.8638 (mm) cc_final: 0.8335 (mt) outliers start: 60 outliers final: 38 residues processed: 295 average time/residue: 0.1249 time to fit residues: 58.7282 Evaluate side-chains 292 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 241 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain B residue 1177 PHE Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 98 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 90 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 38 optimal weight: 0.0070 chunk 131 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 209 optimal weight: 8.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1112 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 739 HIS ** B 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117719 restraints weight = 29497.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.119717 restraints weight = 18617.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121050 restraints weight = 13760.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121459 restraints weight = 10876.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121638 restraints weight = 10409.822| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17691 Z= 0.127 Angle : 0.728 12.430 24093 Z= 0.349 Chirality : 0.045 0.417 2780 Planarity : 0.005 0.081 2984 Dihedral : 7.013 57.269 2970 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 3.31 % Allowed : 23.12 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.19), residues: 2143 helix: 1.18 (0.16), residues: 1169 sheet: -0.99 (0.49), residues: 121 loop : -2.25 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 960 TYR 0.027 0.001 TYR A 224 PHE 0.015 0.001 PHE A 522 TRP 0.021 0.001 TRP A 278 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00278 (17665) covalent geometry : angle 0.71636 (24039) SS BOND : bond 0.00446 ( 6) SS BOND : angle 1.76120 ( 12) hydrogen bonds : bond 0.03412 ( 829) hydrogen bonds : angle 4.02483 ( 2394) metal coordination : bond 0.00179 ( 2) Misc. bond : bond 0.00097 ( 4) link_BETA1-4 : bond 0.00302 ( 2) link_BETA1-4 : angle 1.13532 ( 6) link_NAG-ASN : bond 0.00690 ( 12) link_NAG-ASN : angle 3.26774 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2884.21 seconds wall clock time: 50 minutes 54.96 seconds (3054.96 seconds total)