Starting phenix.real_space_refine on Tue Sep 15 05:28:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6co7_7542/09_2026/6co7_7542.cif Found real_map, /net/cci-nas-00/data/ceres_data/6co7_7542/09_2026/6co7_7542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6co7_7542/09_2026/6co7_7542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6co7_7542/09_2026/6co7_7542.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6co7_7542/09_2026/6co7_7542.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6co7_7542/09_2026/6co7_7542.cif" model { file = "/net/cci-nas-00/data/ceres_data/6co7_7542/09_2026/6co7_7542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6co7_7542/09_2026/6co7_7542.cif" } resolution = 3.07 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 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 20 5.49 5 S 188 5.16 5 Na 3 4.78 5 C 23024 2.51 5 N 5648 2.21 5 O 6368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.18s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35255 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8422 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 41, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 3, 'TYR:plan': 1, 'ASP:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 8422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8422 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 41, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 3, 'TYR:plan': 1, 'ASP:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 8422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8422 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 41, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 3, 'TYR:plan': 1, 'ASP:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 63 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 chiralities: 2 Chain: "A" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 366 Unusual residues: {' CA': 1, ' NA': 3, 'CLR': 1, 'POV': 14} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 8, 'POV:plan-3': 10} Unresolved non-hydrogen planarities: 79 Chain: "B" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 363 Unusual residues: {' CA': 1, 'CLR': 1, 'POV': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-2': 8, 'POV:plan-3': 10, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 363 Unusual residues: {' CA': 1, 'CLR': 1, 'POV': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 10, 'POV:plan-1': 7, 'POV:plan-2': 8} Unresolved non-hydrogen planarities: 79 Restraints were copied for chains: C, F, G, H Time building chain proxies: 15.02, per 1000 atoms: 0.43 Number of scatterers: 35255 At special positions: 0 Unit cell: (149.35, 149.35, 159.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 188 16.00 P 20 15.00 Na 3 11.00 O 6368 8.00 N 5648 7.00 C 23024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 86 " distance=0.00 Simple disulfide: pdb=" SG CYS C 489 " - pdb=" SG CYS C 489 " distance=0.00 Simple disulfide: pdb=" SG CYS C 590 " - pdb=" SG CYS C 590 " distance=0.00 Simple disulfide: pdb=" SG CYS C 655 " - pdb=" SG CYS C 655 " distance=0.00 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 697 " distance=0.00 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 721 " distance=0.00 Simple disulfide: pdb=" SG CYS C 827 " - pdb=" SG CYS C 827 " distance=0.00 Simple disulfide: pdb=" SG CYS C1197 " - pdb=" SG CYS C1197 " distance=0.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A1017 " " NAG F 1 " - " ASN B1017 " " NAG G 1 " - " ASN C1017 " " NAG H 1 " - " ASN D1017 " Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.5 seconds 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8000 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 8 sheets defined 64.8% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.766A pdb=" N VAL A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 171 removed outlier: 4.082A pdb=" N ILE A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 removed outlier: 3.681A pdb=" N HIS A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.647A pdb=" N LEU A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 304 through 316 removed outlier: 4.221A pdb=" N VAL A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 360 through 369 Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.504A pdb=" N THR A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 386 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 420 through 432 removed outlier: 3.665A pdb=" N GLN A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.827A pdb=" N ALA A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 5.294A pdb=" N ALA A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 474 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.708A pdb=" N LEU A 504 " --> pdb=" O THR A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 529 removed outlier: 3.548A pdb=" N VAL A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.508A pdb=" N TYR A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 545 " --> pdb=" O GLY A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 545' Processing helix chain 'A' and resid 578 through 590 Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.588A pdb=" N ALA A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 627 removed outlier: 3.504A pdb=" N ASP A 627 " --> pdb=" O ARG A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 659 Processing helix chain 'A' and resid 659 through 668 removed outlier: 3.705A pdb=" N GLN A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 694 through 706 Processing helix chain 'A' and resid 714 through 724 removed outlier: 3.975A pdb=" N TYR A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 750 removed outlier: 3.595A pdb=" N GLU A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 820 Processing helix chain 'A' and resid 827 through 836 removed outlier: 3.588A pdb=" N MET A 831 " --> pdb=" O CYS A 827 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 833 " --> pdb=" O ARG A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 861 Processing helix chain 'A' and resid 870 through 874 Processing helix chain 'A' and resid 876 through 899 removed outlier: 3.985A pdb=" N ILE A 880 " --> pdb=" O HIS A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 913 Processing helix chain 'A' and resid 916 through 936 removed outlier: 3.722A pdb=" N VAL A 920 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 960 removed outlier: 5.229A pdb=" N ILE A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 970 through 1008 removed outlier: 3.843A pdb=" N LYS A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A 983 " --> pdb=" O GLN A 979 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1035 removed outlier: 3.609A pdb=" N THR A1022 " --> pdb=" O ASN A1018 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A1027 " --> pdb=" O ILE A1023 " (cutoff:3.500A) Proline residue: A1030 - end of helix removed outlier: 3.565A pdb=" N MET A1034 " --> pdb=" O PRO A1030 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR A1035 " --> pdb=" O TYR A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1044 Processing helix chain 'A' and resid 1057 through 1075 Proline residue: A1063 - end of helix removed outlier: 3.543A pdb=" N ILE A1075 " --> pdb=" O VAL A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1114 removed outlier: 4.232A pdb=" N GLU A1090 " --> pdb=" O ASN A1086 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG A1091 " --> pdb=" O TYR A1087 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP A1095 " --> pdb=" O ARG A1091 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A1097 " --> pdb=" O GLN A1093 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS A1098 " --> pdb=" O GLU A1094 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR A1105 " --> pdb=" O LYS A1101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP A1106 " --> pdb=" O PHE A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1136 removed outlier: 3.823A pdb=" N LEU A1128 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A1129 " --> pdb=" O GLY A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1182 Processing helix chain 'A' and resid 1183 through 1210 Processing helix chain 'B' and resid 119 through 129 removed outlier: 3.766A pdb=" N VAL B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 171 removed outlier: 4.081A pdb=" N ILE B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 199 removed outlier: 3.681A pdb=" N HIS B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.648A pdb=" N LEU B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 278 Processing helix chain 'B' and resid 304 through 316 removed outlier: 4.221A pdb=" N VAL B 308 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 316 " --> pdb=" O TYR B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 339 Processing helix chain 'B' and resid 360 through 369 Processing helix chain 'B' and resid 374 through 386 removed outlier: 3.505A pdb=" N THR B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 386 " --> pdb=" O ILE B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 420 through 432 removed outlier: 3.664A pdb=" N GLN B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 441 removed outlier: 3.827A pdb=" N ALA B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 463 removed outlier: 5.294A pdb=" N ALA B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 474 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 500 through 511 removed outlier: 3.709A pdb=" N LEU B 504 " --> pdb=" O THR B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 529 removed outlier: 3.548A pdb=" N VAL B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 545 removed outlier: 3.508A pdb=" N TYR B 544 " --> pdb=" O ASP B 541 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE B 545 " --> pdb=" O GLY B 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 541 through 545' Processing helix chain 'B' and resid 578 through 590 Processing helix chain 'B' and resid 592 through 602 removed outlier: 3.588A pdb=" N ALA B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 627 removed outlier: 3.505A pdb=" N ASP B 627 " --> pdb=" O ARG B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 659 Processing helix chain 'B' and resid 659 through 668 removed outlier: 3.705A pdb=" N GLN B 664 " --> pdb=" O GLU B 660 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 668 " --> pdb=" O GLN B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 686 Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 694 through 706 Processing helix chain 'B' and resid 714 through 724 removed outlier: 3.974A pdb=" N TYR B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 750 removed outlier: 3.595A pdb=" N GLU B 748 " --> pdb=" O ALA B 744 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN B 750 " --> pdb=" O GLU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 820 Processing helix chain 'B' and resid 827 through 836 removed outlier: 3.588A pdb=" N MET B 831 " --> pdb=" O CYS B 827 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 861 Processing helix chain 'B' and resid 870 through 874 Processing helix chain 'B' and resid 876 through 899 removed outlier: 3.985A pdb=" N ILE B 880 " --> pdb=" O HIS B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 913 Processing helix chain 'B' and resid 916 through 936 removed outlier: 3.722A pdb=" N VAL B 920 " --> pdb=" O THR B 916 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE B 936 " --> pdb=" O ILE B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 960 removed outlier: 5.229A pdb=" N ILE B 955 " --> pdb=" O SER B 951 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 970 through 1008 removed outlier: 3.843A pdb=" N LYS B 974 " --> pdb=" O LEU B 970 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN B 979 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN B 983 " --> pdb=" O GLN B 979 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP B 984 " --> pdb=" O LYS B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1035 removed outlier: 3.609A pdb=" N THR B1022 " --> pdb=" O ASN B1018 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B1027 " --> pdb=" O ILE B1023 " (cutoff:3.500A) Proline residue: B1030 - end of helix removed outlier: 3.566A pdb=" N MET B1034 " --> pdb=" O PRO B1030 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR B1035 " --> pdb=" O TYR B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1044 Processing helix chain 'B' and resid 1057 through 1075 Proline residue: B1063 - end of helix removed outlier: 3.543A pdb=" N ILE B1075 " --> pdb=" O VAL B1071 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1114 removed outlier: 4.233A pdb=" N GLU B1090 " --> pdb=" O ASN B1086 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG B1091 " --> pdb=" O TYR B1087 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B1095 " --> pdb=" O ARG B1091 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP B1097 " --> pdb=" O GLN B1093 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS B1098 " --> pdb=" O GLU B1094 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR B1105 " --> pdb=" O LYS B1101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP B1106 " --> pdb=" O PHE B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1136 removed outlier: 3.823A pdb=" N LEU B1128 " --> pdb=" O LEU B1124 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B1129 " --> pdb=" O GLY B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1154 through 1182 Processing helix chain 'B' and resid 1183 through 1210 Processing helix chain 'C' and resid 119 through 129 removed outlier: 3.766A pdb=" N VAL C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 171 removed outlier: 4.081A pdb=" N ILE C 164 " --> pdb=" O ARG C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 199 removed outlier: 3.681A pdb=" N HIS C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.647A pdb=" N LEU C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 278 Processing helix chain 'C' and resid 304 through 316 removed outlier: 4.221A pdb=" N VAL C 308 " --> pdb=" O GLY C 304 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS C 316 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 339 Processing helix chain 'C' and resid 360 through 369 Processing helix chain 'C' and resid 374 through 386 removed outlier: 3.503A pdb=" N THR C 378 " --> pdb=" O GLY C 374 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 386 " --> pdb=" O ILE C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 417 Processing helix chain 'C' and resid 420 through 432 removed outlier: 3.665A pdb=" N GLN C 424 " --> pdb=" O SER C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.828A pdb=" N ALA C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 463 removed outlier: 5.293A pdb=" N ALA C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA C 456 " --> pdb=" O THR C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 474 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 500 through 511 removed outlier: 3.708A pdb=" N LEU C 504 " --> pdb=" O THR C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 529 removed outlier: 3.547A pdb=" N VAL C 522 " --> pdb=" O ASP C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 545 removed outlier: 3.508A pdb=" N TYR C 544 " --> pdb=" O ASP C 541 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 545 " --> pdb=" O GLY C 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 541 through 545' Processing helix chain 'C' and resid 578 through 590 Processing helix chain 'C' and resid 592 through 602 removed outlier: 3.588A pdb=" N ALA C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 627 removed outlier: 3.504A pdb=" N ASP C 627 " --> pdb=" O ARG C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 659 Processing helix chain 'C' and resid 659 through 668 removed outlier: 3.705A pdb=" N GLN C 664 " --> pdb=" O GLU C 660 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 686 Processing helix chain 'C' and resid 688 through 693 Processing helix chain 'C' and resid 694 through 706 Processing helix chain 'C' and resid 714 through 724 removed outlier: 3.975A pdb=" N TYR C 723 " --> pdb=" O LEU C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 750 removed outlier: 3.595A pdb=" N GLU C 748 " --> pdb=" O ALA C 744 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN C 750 " --> pdb=" O GLU C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 820 Processing helix chain 'C' and resid 827 through 836 removed outlier: 3.587A pdb=" N MET C 831 " --> pdb=" O CYS C 827 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE C 833 " --> pdb=" O ARG C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 861 Processing helix chain 'C' and resid 870 through 874 Processing helix chain 'C' and resid 876 through 899 removed outlier: 3.985A pdb=" N ILE C 880 " --> pdb=" O HIS C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 913 Processing helix chain 'C' and resid 916 through 936 removed outlier: 3.721A pdb=" N VAL C 920 " --> pdb=" O THR C 916 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE C 936 " --> pdb=" O ILE C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 960 removed outlier: 5.229A pdb=" N ILE C 955 " --> pdb=" O SER C 951 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 970 through 1008 removed outlier: 3.843A pdb=" N LYS C 974 " --> pdb=" O LEU C 970 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN C 979 " --> pdb=" O LEU C 975 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN C 983 " --> pdb=" O GLN C 979 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP C 984 " --> pdb=" O LYS C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1035 removed outlier: 3.608A pdb=" N THR C1022 " --> pdb=" O ASN C1018 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL C1027 " --> pdb=" O ILE C1023 " (cutoff:3.500A) Proline residue: C1030 - end of helix removed outlier: 3.565A pdb=" N MET C1034 " --> pdb=" O PRO C1030 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR C1035 " --> pdb=" O TYR C1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1044 Processing helix chain 'C' and resid 1057 through 1075 Proline residue: C1063 - end of helix removed outlier: 3.543A pdb=" N ILE C1075 " --> pdb=" O VAL C1071 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1114 removed outlier: 4.231A pdb=" N GLU C1090 " --> pdb=" O ASN C1086 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG C1091 " --> pdb=" O TYR C1087 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP C1095 " --> pdb=" O ARG C1091 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP C1097 " --> pdb=" O GLN C1093 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS C1098 " --> pdb=" O GLU C1094 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR C1105 " --> pdb=" O LYS C1101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP C1106 " --> pdb=" O PHE C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1121 through 1136 removed outlier: 3.823A pdb=" N LEU C1128 " --> pdb=" O LEU C1124 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE C1129 " --> pdb=" O GLY C1125 " (cutoff:3.500A) Processing helix chain 'C' and resid 1154 through 1182 Processing helix chain 'C' and resid 1183 through 1210 Processing helix chain 'D' and resid 119 through 129 removed outlier: 3.766A pdb=" N VAL D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 171 removed outlier: 4.082A pdb=" N ILE D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 199 removed outlier: 3.681A pdb=" N HIS D 186 " --> pdb=" O GLY D 182 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 removed outlier: 3.647A pdb=" N LEU D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 278 Processing helix chain 'D' and resid 304 through 316 removed outlier: 4.220A pdb=" N VAL D 308 " --> pdb=" O GLY D 304 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS D 316 " --> pdb=" O TYR D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 339 Processing helix chain 'D' and resid 360 through 369 Processing helix chain 'D' and resid 374 through 386 removed outlier: 3.503A pdb=" N THR D 378 " --> pdb=" O GLY D 374 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 386 " --> pdb=" O ILE D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 417 Processing helix chain 'D' and resid 420 through 432 removed outlier: 3.665A pdb=" N GLN D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 441 removed outlier: 3.828A pdb=" N ALA D 437 " --> pdb=" O ARG D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 463 removed outlier: 5.294A pdb=" N ALA D 455 " --> pdb=" O GLU D 451 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA D 456 " --> pdb=" O THR D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 474 Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 500 through 511 removed outlier: 3.708A pdb=" N LEU D 504 " --> pdb=" O THR D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 529 removed outlier: 3.547A pdb=" N VAL D 522 " --> pdb=" O ASP D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 545 removed outlier: 3.508A pdb=" N TYR D 544 " --> pdb=" O ASP D 541 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 545 " --> pdb=" O GLY D 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 541 through 545' Processing helix chain 'D' and resid 578 through 590 Processing helix chain 'D' and resid 592 through 602 removed outlier: 3.588A pdb=" N ALA D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 627 removed outlier: 3.504A pdb=" N ASP D 627 " --> pdb=" O ARG D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 659 Processing helix chain 'D' and resid 659 through 668 removed outlier: 3.705A pdb=" N GLN D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 668 " --> pdb=" O GLN D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 686 Processing helix chain 'D' and resid 688 through 693 Processing helix chain 'D' and resid 694 through 706 Processing helix chain 'D' and resid 714 through 724 removed outlier: 3.974A pdb=" N TYR D 723 " --> pdb=" O LEU D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 750 removed outlier: 3.595A pdb=" N GLU D 748 " --> pdb=" O ALA D 744 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN D 750 " --> pdb=" O GLU D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 820 Processing helix chain 'D' and resid 827 through 836 removed outlier: 3.587A pdb=" N MET D 831 " --> pdb=" O CYS D 827 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE D 833 " --> pdb=" O ARG D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 836 through 861 Processing helix chain 'D' and resid 870 through 874 Processing helix chain 'D' and resid 876 through 899 removed outlier: 3.985A pdb=" N ILE D 880 " --> pdb=" O HIS D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 913 Processing helix chain 'D' and resid 916 through 936 removed outlier: 3.722A pdb=" N VAL D 920 " --> pdb=" O THR D 916 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE D 936 " --> pdb=" O ILE D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 960 removed outlier: 5.229A pdb=" N ILE D 955 " --> pdb=" O SER D 951 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE D 956 " --> pdb=" O LEU D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 966 Processing helix chain 'D' and resid 970 through 1008 removed outlier: 3.843A pdb=" N LYS D 974 " --> pdb=" O LEU D 970 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN D 979 " --> pdb=" O LEU D 975 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN D 983 " --> pdb=" O GLN D 979 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP D 984 " --> pdb=" O LYS D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1018 through 1035 removed outlier: 3.608A pdb=" N THR D1022 " --> pdb=" O ASN D1018 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL D1027 " --> pdb=" O ILE D1023 " (cutoff:3.500A) Proline residue: D1030 - end of helix removed outlier: 3.566A pdb=" N MET D1034 " --> pdb=" O PRO D1030 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR D1035 " --> pdb=" O TYR D1031 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1044 Processing helix chain 'D' and resid 1057 through 1075 Proline residue: D1063 - end of helix removed outlier: 3.543A pdb=" N ILE D1075 " --> pdb=" O VAL D1071 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1114 removed outlier: 4.232A pdb=" N GLU D1090 " --> pdb=" O ASN D1086 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG D1091 " --> pdb=" O TYR D1087 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP D1095 " --> pdb=" O ARG D1091 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP D1097 " --> pdb=" O GLN D1093 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS D1098 " --> pdb=" O GLU D1094 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR D1105 " --> pdb=" O LYS D1101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP D1106 " --> pdb=" O PHE D1102 " (cutoff:3.500A) Processing helix chain 'D' and resid 1121 through 1136 removed outlier: 3.824A pdb=" N LEU D1128 " --> pdb=" O LEU D1124 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE D1129 " --> pdb=" O GLY D1125 " (cutoff:3.500A) Processing helix chain 'D' and resid 1154 through 1182 Processing helix chain 'D' and resid 1183 through 1210 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 233 removed outlier: 6.922A pdb=" N TYR A 233 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP A 99 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N PHE A 253 " --> pdb=" O ARG A 108 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LEU A 255 " --> pdb=" O PRO A 110 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 112 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP A 257 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N MET A 114 " --> pdb=" O ASP A 257 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N VAL A 322 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 298 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE A 324 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL A 300 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 48 Processing sheet with id=AA4, first strand: chain 'B' and resid 232 through 233 removed outlier: 6.922A pdb=" N TYR B 233 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP B 99 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N PHE B 253 " --> pdb=" O ARG B 108 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LEU B 255 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU B 112 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP B 257 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N MET B 114 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N VAL B 322 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 298 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE B 324 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL B 300 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 46 through 48 Processing sheet with id=AA6, first strand: chain 'C' and resid 232 through 233 removed outlier: 6.922A pdb=" N TYR C 233 " --> pdb=" O GLU C 97 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP C 99 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N PHE C 253 " --> pdb=" O ARG C 108 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LEU C 255 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU C 112 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP C 257 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N MET C 114 " --> pdb=" O ASP C 257 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N VAL C 322 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 298 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE C 324 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL C 300 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 46 through 48 Processing sheet with id=AA8, first strand: chain 'D' and resid 232 through 233 removed outlier: 6.921A pdb=" N TYR D 233 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP D 99 " --> pdb=" O TYR D 233 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N PHE D 253 " --> pdb=" O ARG D 108 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LEU D 255 " --> pdb=" O PRO D 110 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU D 112 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP D 257 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N MET D 114 " --> pdb=" O ASP D 257 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N VAL D 322 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU D 298 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE D 324 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL D 300 " --> pdb=" O ILE D 324 " (cutoff:3.500A) 1892 hydrogen bonds defined for protein. 5640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.30 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5620 1.31 - 1.43: 8968 1.43 - 1.56: 20904 1.56 - 1.68: 88 1.68 - 1.81: 344 Bond restraints: 35924 Sorted by residual: bond pdb=" C MET C1007 " pdb=" N PHE C1008 " ideal model delta sigma weight residual 1.330 1.481 -0.151 1.21e-02 6.83e+03 1.56e+02 bond pdb=" C MET A1007 " pdb=" N PHE A1008 " ideal model delta sigma weight residual 1.330 1.481 -0.150 1.21e-02 6.83e+03 1.54e+02 bond pdb=" C MET D1007 " pdb=" N PHE D1008 " ideal model delta sigma weight residual 1.330 1.481 -0.150 1.21e-02 6.83e+03 1.54e+02 bond pdb=" C MET B1007 " pdb=" N PHE B1008 " ideal model delta sigma weight residual 1.330 1.480 -0.150 1.21e-02 6.83e+03 1.53e+02 bond pdb=" C29 POV B3004 " pdb="C210 POV B3004 " ideal model delta sigma weight residual 1.333 1.535 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 35919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.06: 47684 4.06 - 8.13: 516 8.13 - 12.19: 40 12.19 - 16.26: 68 16.26 - 20.32: 20 Bond angle restraints: 48328 Sorted by residual: angle pdb=" N PRO B 8 " pdb=" CA PRO B 8 " pdb=" CB PRO B 8 " ideal model delta sigma weight residual 103.36 110.44 -7.08 8.80e-01 1.29e+00 6.47e+01 angle pdb=" N PRO C 8 " pdb=" CA PRO C 8 " pdb=" CB PRO C 8 " ideal model delta sigma weight residual 103.36 110.44 -7.08 8.80e-01 1.29e+00 6.47e+01 angle pdb=" N PRO D 8 " pdb=" CA PRO D 8 " pdb=" CB PRO D 8 " ideal model delta sigma weight residual 103.36 110.42 -7.06 8.80e-01 1.29e+00 6.44e+01 angle pdb=" N PRO A 8 " pdb=" CA PRO A 8 " pdb=" CB PRO A 8 " ideal model delta sigma weight residual 103.36 110.42 -7.06 8.80e-01 1.29e+00 6.43e+01 angle pdb=" N PRO D 50 " pdb=" CA PRO D 50 " pdb=" CB PRO D 50 " ideal model delta sigma weight residual 103.25 110.60 -7.35 1.05e+00 9.07e-01 4.90e+01 ... (remaining 48323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 20603 22.35 - 44.70: 789 44.70 - 67.05: 124 67.05 - 89.40: 28 89.40 - 111.75: 16 Dihedral angle restraints: 21560 sinusoidal: 9192 harmonic: 12368 Sorted by residual: dihedral pdb=" CA SER C1010 " pdb=" C SER C1010 " pdb=" N PRO C1011 " pdb=" CA PRO C1011 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER A1010 " pdb=" C SER A1010 " pdb=" N PRO A1011 " pdb=" CA PRO A1011 " ideal model delta harmonic sigma weight residual 180.00 152.77 27.23 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER D1010 " pdb=" C SER D1010 " pdb=" N PRO D1011 " pdb=" CA PRO D1011 " ideal model delta harmonic sigma weight residual 180.00 152.77 27.23 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 21557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3634 0.058 - 0.115: 1339 0.115 - 0.173: 305 0.173 - 0.231: 88 0.231 - 0.289: 10 Chirality restraints: 5376 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.97e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.94e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.76e+00 ... (remaining 5373 not shown) Planarity restraints: 5996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A3011 " 0.147 2.00e-02 2.50e+03 2.66e-01 7.08e+02 pdb=" C29 POV A3011 " -0.351 2.00e-02 2.50e+03 pdb="C210 POV A3011 " 0.345 2.00e-02 2.50e+03 pdb="C211 POV A3011 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C3011 " -0.146 2.00e-02 2.50e+03 2.66e-01 7.08e+02 pdb=" C29 POV C3011 " 0.351 2.00e-02 2.50e+03 pdb="C210 POV C3011 " -0.345 2.00e-02 2.50e+03 pdb="C211 POV C3011 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B3011 " 0.147 2.00e-02 2.50e+03 2.66e-01 7.08e+02 pdb=" C29 POV B3011 " -0.351 2.00e-02 2.50e+03 pdb="C210 POV B3011 " 0.345 2.00e-02 2.50e+03 pdb="C211 POV B3011 " -0.140 2.00e-02 2.50e+03 ... (remaining 5993 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 76 2.64 - 3.20: 29442 3.20 - 3.77: 51212 3.77 - 4.33: 71784 4.33 - 4.90: 119760 Nonbonded interactions: 272274 Sorted by model distance: nonbonded pdb="NA NA A4001 " pdb="NA NA A4002 " model vdw 2.070 1.900 nonbonded pdb=" O VAL B 859 " pdb=" OG SER C1010 " model vdw 2.384 3.040 nonbonded pdb=" O VAL A 859 " pdb=" OG SER B1010 " model vdw 2.384 3.040 nonbonded pdb=" O VAL C 859 " pdb=" OG SER D1010 " model vdw 2.390 3.040 nonbonded pdb=" OG SER A1010 " pdb=" O VAL D 859 " model vdw 2.393 3.040 ... (remaining 272269 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 6 through 1210 or (resid 3002 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C310 or name C311 or name C312 or name C313 or name C314 or name C315) \ ) or (resid 3004 and (name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C210 or name C211 or name C212 or name C213)) or (resid 3006 \ and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39)) or resid 3007 or resid 3009)) selection = (chain 'B' and (resid 6 through 1210 or (resid 3001 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C310 or name C311 or name C312 or name C313 or name C314 or name C315) \ ) or (resid 3003 and (name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C210 or name C211 or name C212 or name C213)) or (resid 3005 \ and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39)) or resid 3006 or (resid 3008 and (name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C310 or name C311 or name C312)))) selection = (chain 'C' and (resid 6 through 1210 or (resid 3001 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C310 or name C311 or name C312 or name C313 or name C314 or name C315) \ ) or (resid 3003 and (name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C210 or name C211 or name C212 or name C213)) or (resid 3005 \ and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39)) or resid 3006 or (resid 3008 and (name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C310 or name C311 or name C312)))) selection = (chain 'D' and (resid 6 through 1210 or (resid 3012 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C310 or name C311 or name C312 or name C313 or name C314 or name C315) \ ) or (resid 3014 and (name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C210 or name C211 or name C212 or name C213)) or (resid 3001 \ and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39)) or (resid 3002 and (name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C310 or name C311 or name C312 or name C313 or name C314 or name C315 or na \ me C316)) or (resid 3004 and (name C31 or name C32 or name C33 or name C34 or na \ me C35 or name C36 or name C37 or name C38 or name C39 or name C310 or name C311 \ or name C312)))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 39.860 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.090 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5130 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 0.202 35932 Z= 0.667 Angle : 1.391 20.322 48360 Z= 0.794 Chirality : 0.064 0.289 5376 Planarity : 0.012 0.266 5992 Dihedral : 13.186 111.750 13544 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.60 % Favored : 94.30 % Rotamer: Outliers : 0.33 % Allowed : 2.44 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.11), residues: 4196 helix: -0.51 (0.09), residues: 2544 sheet: -1.65 (0.31), residues: 180 loop : -2.67 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1059 TYR 0.012 0.001 TYR B 229 PHE 0.015 0.002 PHE D1085 TRP 0.018 0.001 TRP C 885 HIS 0.004 0.001 HIS D1126 Details of bonding type rmsd/Z covalent geometry : bond 0.01067 / 0.67 (35924) covalent geometry : angle 1.39030 / 0.79 (48328) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.19036 / 12.94 ( 1892) hydrogen bonds : angle 6.82390 / 4.83 ( 5640) link_BETA1-4 : bond 0.00151 / 0.08 ( 4) link_BETA1-4 : angle 2.84930 / 1.73 ( 12) link_NAG-ASN : bond 0.00220 / 0.11 ( 4) link_NAG-ASN : angle 1.77823 / 1.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 784 time to evaluate : 1.361 Fit side-chains REVERT: A 107 LYS cc_start: 0.6801 (mttm) cc_final: 0.6510 (pttp) REVERT: A 112 LEU cc_start: 0.6264 (tt) cc_final: 0.6026 (tt) REVERT: A 158 MET cc_start: 0.6500 (ttm) cc_final: 0.6268 (tpp) REVERT: A 184 MET cc_start: 0.5139 (mpp) cc_final: 0.4869 (mtm) REVERT: A 220 ASP cc_start: 0.7262 (t70) cc_final: 0.6990 (t0) REVERT: A 260 THR cc_start: 0.7684 (p) cc_final: 0.7472 (p) REVERT: A 270 MET cc_start: 0.6015 (tpp) cc_final: 0.5677 (tpt) REVERT: A 343 LYS cc_start: 0.5108 (tmtp) cc_final: 0.4903 (tptp) REVERT: A 344 ARG cc_start: 0.7754 (mpp-170) cc_final: 0.7104 (ttp80) REVERT: A 383 LYS cc_start: 0.6399 (pttt) cc_final: 0.6179 (ptpt) REVERT: A 387 GLU cc_start: 0.5014 (tp30) cc_final: 0.4476 (tm-30) REVERT: A 389 GLU cc_start: 0.7323 (tp30) cc_final: 0.6769 (mt-10) REVERT: A 444 GLU cc_start: 0.7932 (pm20) cc_final: 0.7338 (mt-10) REVERT: A 445 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7326 (tp30) REVERT: A 481 GLU cc_start: 0.5667 (mp0) cc_final: 0.5094 (mp0) REVERT: A 545 PHE cc_start: 0.6062 (m-80) cc_final: 0.5851 (m-80) REVERT: A 626 GLU cc_start: 0.6189 (pt0) cc_final: 0.5978 (pp20) REVERT: A 676 ARG cc_start: 0.6976 (mtt-85) cc_final: 0.6597 (mmm-85) REVERT: A 1128 LEU cc_start: 0.5464 (mt) cc_final: 0.5240 (mt) REVERT: A 1132 ARG cc_start: 0.5791 (ttp-170) cc_final: 0.5010 (mtt-85) REVERT: A 1161 MET cc_start: 0.4885 (mmm) cc_final: 0.4579 (mmt) REVERT: B 107 LYS cc_start: 0.6812 (mttm) cc_final: 0.6517 (pttp) REVERT: B 112 LEU cc_start: 0.6189 (tt) cc_final: 0.5955 (tt) REVERT: B 158 MET cc_start: 0.6497 (ttm) cc_final: 0.6288 (tpp) REVERT: B 184 MET cc_start: 0.5134 (mpp) cc_final: 0.4876 (mtm) REVERT: B 220 ASP cc_start: 0.7262 (t70) cc_final: 0.6990 (t0) REVERT: B 260 THR cc_start: 0.7688 (p) cc_final: 0.7476 (p) REVERT: B 270 MET cc_start: 0.6021 (tpp) cc_final: 0.5677 (tpt) REVERT: B 343 LYS cc_start: 0.5091 (tmtp) cc_final: 0.4886 (tptp) REVERT: B 344 ARG cc_start: 0.7732 (mpp-170) cc_final: 0.7100 (ttp80) REVERT: B 383 LYS cc_start: 0.6395 (pttt) cc_final: 0.6175 (ptpt) REVERT: B 387 GLU cc_start: 0.5017 (tp30) cc_final: 0.4479 (tm-30) REVERT: B 389 GLU cc_start: 0.7324 (tp30) cc_final: 0.6769 (mt-10) REVERT: B 444 GLU cc_start: 0.7910 (pm20) cc_final: 0.7308 (mt-10) REVERT: B 445 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7316 (tp30) REVERT: B 481 GLU cc_start: 0.5690 (mp0) cc_final: 0.5093 (mp0) REVERT: B 490 LYS cc_start: 0.5820 (ttmp) cc_final: 0.5611 (tttp) REVERT: B 533 MET cc_start: 0.6928 (mtp) cc_final: 0.6723 (mmm) REVERT: B 670 GLU cc_start: 0.6685 (tt0) cc_final: 0.5896 (tm-30) REVERT: B 676 ARG cc_start: 0.6979 (mtt-85) cc_final: 0.6017 (mtm110) REVERT: B 1128 LEU cc_start: 0.5440 (mt) cc_final: 0.5211 (mt) REVERT: B 1132 ARG cc_start: 0.5817 (ttp-170) cc_final: 0.5029 (mtt-85) REVERT: B 1161 MET cc_start: 0.4897 (mmm) cc_final: 0.4585 (mmt) REVERT: C 107 LYS cc_start: 0.6748 (mttm) cc_final: 0.6461 (pttp) REVERT: C 112 LEU cc_start: 0.6190 (tt) cc_final: 0.5963 (tt) REVERT: C 158 MET cc_start: 0.6403 (ttm) cc_final: 0.6173 (tpp) REVERT: C 184 MET cc_start: 0.5140 (mpp) cc_final: 0.4882 (mtm) REVERT: C 220 ASP cc_start: 0.7262 (t70) cc_final: 0.6983 (t0) REVERT: C 260 THR cc_start: 0.7691 (p) cc_final: 0.7480 (p) REVERT: C 270 MET cc_start: 0.5984 (tpp) cc_final: 0.5444 (tpt) REVERT: C 343 LYS cc_start: 0.5066 (tmtp) cc_final: 0.4858 (tptp) REVERT: C 344 ARG cc_start: 0.7733 (mpp-170) cc_final: 0.7099 (ttp80) REVERT: C 383 LYS cc_start: 0.6405 (pttt) cc_final: 0.6187 (ptpt) REVERT: C 387 GLU cc_start: 0.5022 (tp30) cc_final: 0.4486 (tm-30) REVERT: C 389 GLU cc_start: 0.7348 (tp30) cc_final: 0.6767 (mt-10) REVERT: C 444 GLU cc_start: 0.7911 (pm20) cc_final: 0.7308 (mt-10) REVERT: C 445 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7304 (tp30) REVERT: C 481 GLU cc_start: 0.5774 (mp0) cc_final: 0.5162 (mp0) REVERT: C 490 LYS cc_start: 0.5826 (ttmp) cc_final: 0.5615 (tttp) REVERT: C 676 ARG cc_start: 0.7003 (mtt-85) cc_final: 0.6155 (mtm110) REVERT: C 1053 GLU cc_start: 0.6762 (pt0) cc_final: 0.6328 (mt-10) REVERT: C 1128 LEU cc_start: 0.5332 (mt) cc_final: 0.5111 (mt) REVERT: C 1132 ARG cc_start: 0.5749 (ttp-170) cc_final: 0.5015 (mtt-85) REVERT: C 1161 MET cc_start: 0.4858 (mmm) cc_final: 0.4535 (mmt) REVERT: D 107 LYS cc_start: 0.6743 (mttm) cc_final: 0.6441 (pttp) REVERT: D 112 LEU cc_start: 0.6279 (tt) cc_final: 0.6072 (tt) REVERT: D 158 MET cc_start: 0.6501 (ttm) cc_final: 0.6293 (tpp) REVERT: D 184 MET cc_start: 0.5137 (mpp) cc_final: 0.4873 (mtm) REVERT: D 220 ASP cc_start: 0.7314 (t70) cc_final: 0.7031 (t0) REVERT: D 260 THR cc_start: 0.7684 (p) cc_final: 0.7471 (p) REVERT: D 270 MET cc_start: 0.6032 (tpp) cc_final: 0.5686 (tpt) REVERT: D 343 LYS cc_start: 0.5101 (tmtp) cc_final: 0.4895 (tptp) REVERT: D 344 ARG cc_start: 0.7749 (mpp-170) cc_final: 0.7108 (ttp80) REVERT: D 383 LYS cc_start: 0.6410 (pttt) cc_final: 0.6191 (ptpt) REVERT: D 387 GLU cc_start: 0.5022 (tp30) cc_final: 0.4485 (tm-30) REVERT: D 389 GLU cc_start: 0.7339 (tp30) cc_final: 0.6761 (mt-10) REVERT: D 444 GLU cc_start: 0.7921 (pm20) cc_final: 0.7328 (mt-10) REVERT: D 445 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7314 (tp30) REVERT: D 481 GLU cc_start: 0.5757 (mp0) cc_final: 0.5177 (mp0) REVERT: D 490 LYS cc_start: 0.5833 (ttmp) cc_final: 0.5622 (tttp) REVERT: D 626 GLU cc_start: 0.6201 (pt0) cc_final: 0.5988 (pp20) REVERT: D 676 ARG cc_start: 0.7000 (mtt-85) cc_final: 0.6635 (mmm-85) REVERT: D 1128 LEU cc_start: 0.5334 (mt) cc_final: 0.5115 (mt) REVERT: D 1132 ARG cc_start: 0.5776 (ttp-170) cc_final: 0.5040 (mtt-85) REVERT: D 1161 MET cc_start: 0.4899 (mmm) cc_final: 0.4574 (mmt) outliers start: 12 outliers final: 4 residues processed: 791 average time/residue: 0.2604 time to fit residues: 321.4048 Evaluate side-chains 458 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 454 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 353 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.106567 restraints weight = 43340.195| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.75 r_work: 0.2988 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35932 Z= 0.140 Angle : 0.582 8.394 48360 Z= 0.302 Chirality : 0.042 0.161 5376 Planarity : 0.004 0.049 5992 Dihedral : 11.567 97.322 5548 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.36 % Favored : 96.54 % Rotamer: Outliers : 0.67 % Allowed : 7.44 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.13), residues: 4196 helix: 1.01 (0.10), residues: 2560 sheet: -1.23 (0.30), residues: 208 loop : -2.38 (0.14), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1194 TYR 0.028 0.001 TYR D 312 PHE 0.011 0.001 PHE A 584 TRP 0.011 0.001 TRP B 705 HIS 0.003 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (35924) covalent geometry : angle 0.58101 / 0.30 (48328) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.05900 / 3.92 ( 1892) hydrogen bonds : angle 4.49385 / 3.20 ( 5640) link_BETA1-4 : bond 0.00576 / 0.29 ( 4) link_BETA1-4 : angle 1.73405 / 1.07 ( 12) link_NAG-ASN : bond 0.00215 / 0.11 ( 4) link_NAG-ASN : angle 0.91401 / 0.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 526 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.7751 (mtm) cc_final: 0.7100 (mtp) REVERT: A 220 ASP cc_start: 0.8184 (t70) cc_final: 0.7960 (t0) REVERT: A 276 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7599 (tp30) REVERT: A 383 LYS cc_start: 0.7695 (pttt) cc_final: 0.7311 (ptpt) REVERT: A 387 GLU cc_start: 0.7195 (tp30) cc_final: 0.6429 (tm-30) REVERT: A 444 GLU cc_start: 0.8190 (pm20) cc_final: 0.7973 (mt-10) REVERT: A 445 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7636 (tp30) REVERT: A 626 GLU cc_start: 0.8123 (pt0) cc_final: 0.7688 (pp20) REVERT: A 1132 ARG cc_start: 0.7501 (ttp-170) cc_final: 0.5907 (mmt180) REVERT: B 197 MET cc_start: 0.7762 (mtm) cc_final: 0.7101 (mtp) REVERT: B 220 ASP cc_start: 0.8200 (t70) cc_final: 0.7971 (t0) REVERT: B 276 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7616 (tp30) REVERT: B 383 LYS cc_start: 0.7683 (pttt) cc_final: 0.7301 (ptpt) REVERT: B 387 GLU cc_start: 0.7155 (tp30) cc_final: 0.6285 (tm-30) REVERT: B 444 GLU cc_start: 0.8220 (pm20) cc_final: 0.8000 (mt-10) REVERT: B 445 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7636 (tp30) REVERT: B 490 LYS cc_start: 0.8822 (ttmp) cc_final: 0.8506 (tttp) REVERT: B 676 ARG cc_start: 0.8342 (mtt-85) cc_final: 0.7968 (mtm110) REVERT: B 1132 ARG cc_start: 0.7535 (ttp-170) cc_final: 0.5931 (mmt180) REVERT: C 197 MET cc_start: 0.7765 (mtm) cc_final: 0.7080 (mtp) REVERT: C 276 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7628 (tp30) REVERT: C 383 LYS cc_start: 0.7653 (pttt) cc_final: 0.7291 (ptpt) REVERT: C 387 GLU cc_start: 0.7169 (tp30) cc_final: 0.6296 (tm-30) REVERT: C 444 GLU cc_start: 0.8215 (pm20) cc_final: 0.7996 (mt-10) REVERT: C 445 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7632 (tp30) REVERT: C 490 LYS cc_start: 0.8793 (ttmp) cc_final: 0.8470 (tttp) REVERT: C 1132 ARG cc_start: 0.7585 (ttp-170) cc_final: 0.5971 (mmt180) REVERT: D 197 MET cc_start: 0.7769 (mtm) cc_final: 0.7091 (mtp) REVERT: D 276 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7608 (tp30) REVERT: D 383 LYS cc_start: 0.7654 (pttt) cc_final: 0.7229 (ptpt) REVERT: D 387 GLU cc_start: 0.7156 (tp30) cc_final: 0.6278 (tm-30) REVERT: D 389 GLU cc_start: 0.8007 (tp30) cc_final: 0.7764 (tp30) REVERT: D 444 GLU cc_start: 0.8247 (pm20) cc_final: 0.8017 (mt-10) REVERT: D 445 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7635 (tp30) REVERT: D 490 LYS cc_start: 0.8821 (ttmp) cc_final: 0.8495 (tttp) REVERT: D 626 GLU cc_start: 0.8161 (pt0) cc_final: 0.7726 (pp20) REVERT: D 1132 ARG cc_start: 0.7565 (ttp-170) cc_final: 0.5952 (mmt180) outliers start: 24 outliers final: 17 residues processed: 540 average time/residue: 0.2564 time to fit residues: 219.1380 Evaluate side-chains 461 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 444 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 827 CYS Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 827 CYS Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 1107 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 1107 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 166 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 225 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 348 optimal weight: 0.4980 chunk 313 optimal weight: 4.9990 chunk 378 optimal weight: 3.9990 chunk 369 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 HIS B 250 HIS C 250 HIS D 250 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.140533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.103077 restraints weight = 43569.005| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.86 r_work: 0.2943 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35932 Z= 0.168 Angle : 0.579 7.684 48360 Z= 0.297 Chirality : 0.042 0.154 5376 Planarity : 0.005 0.045 5992 Dihedral : 10.815 91.053 5548 Min Nonbonded Distance : 1.630 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 1.64 % Allowed : 8.03 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.13), residues: 4196 helix: 1.26 (0.10), residues: 2580 sheet: -1.23 (0.30), residues: 256 loop : -2.13 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1194 TYR 0.016 0.002 TYR A 855 PHE 0.015 0.001 PHE C 584 TRP 0.010 0.001 TRP B 705 HIS 0.005 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (35924) covalent geometry : angle 0.57838 / 0.30 (48328) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.05840 / 3.88 ( 1892) hydrogen bonds : angle 4.25162 / 3.03 ( 5640) link_BETA1-4 : bond 0.00228 / 0.12 ( 4) link_BETA1-4 : angle 1.90964 / 1.15 ( 12) link_NAG-ASN : bond 0.00222 / 0.11 ( 4) link_NAG-ASN : angle 1.43660 / 0.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 458 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.7861 (mtm) cc_final: 0.7229 (mtp) REVERT: A 220 ASP cc_start: 0.8191 (t70) cc_final: 0.7872 (t0) REVERT: A 276 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7485 (tp30) REVERT: A 383 LYS cc_start: 0.7773 (pttt) cc_final: 0.7347 (ptpt) REVERT: A 387 GLU cc_start: 0.7090 (tp30) cc_final: 0.6290 (tm-30) REVERT: A 389 GLU cc_start: 0.7915 (tt0) cc_final: 0.7567 (tp30) REVERT: A 444 GLU cc_start: 0.8248 (pm20) cc_final: 0.7964 (mt-10) REVERT: A 445 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7585 (tp30) REVERT: A 626 GLU cc_start: 0.8030 (pt0) cc_final: 0.7502 (pp20) REVERT: A 1132 ARG cc_start: 0.7524 (ttp-170) cc_final: 0.5883 (mmt180) REVERT: B 197 MET cc_start: 0.7865 (mtm) cc_final: 0.7229 (mtp) REVERT: B 220 ASP cc_start: 0.8202 (t70) cc_final: 0.7884 (t0) REVERT: B 276 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7491 (tp30) REVERT: B 383 LYS cc_start: 0.7777 (pttt) cc_final: 0.7352 (ptpt) REVERT: B 387 GLU cc_start: 0.7099 (tp30) cc_final: 0.6296 (tm-30) REVERT: B 389 GLU cc_start: 0.7931 (tt0) cc_final: 0.7545 (tp30) REVERT: B 444 GLU cc_start: 0.8247 (pm20) cc_final: 0.7954 (mt-10) REVERT: B 445 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7584 (tp30) REVERT: B 490 LYS cc_start: 0.8708 (ttmp) cc_final: 0.8323 (tttp) REVERT: B 1132 ARG cc_start: 0.7482 (ttp-170) cc_final: 0.5869 (mmt180) REVERT: C 197 MET cc_start: 0.7857 (mtm) cc_final: 0.7208 (mtp) REVERT: C 276 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7519 (tp30) REVERT: C 310 THR cc_start: 0.8081 (m) cc_final: 0.7846 (p) REVERT: C 383 LYS cc_start: 0.7641 (pttt) cc_final: 0.7200 (ptpt) REVERT: C 387 GLU cc_start: 0.7110 (tp30) cc_final: 0.6294 (tm-30) REVERT: C 389 GLU cc_start: 0.7948 (tt0) cc_final: 0.7562 (tp30) REVERT: C 444 GLU cc_start: 0.8232 (pm20) cc_final: 0.7951 (mt-10) REVERT: C 445 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7366 (tp30) REVERT: C 490 LYS cc_start: 0.8698 (ttmp) cc_final: 0.8312 (tttp) REVERT: C 1132 ARG cc_start: 0.7492 (ttp-170) cc_final: 0.5864 (mmt180) REVERT: D 197 MET cc_start: 0.7839 (mtm) cc_final: 0.7187 (mtp) REVERT: D 276 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7511 (tp30) REVERT: D 310 THR cc_start: 0.8120 (m) cc_final: 0.7870 (p) REVERT: D 383 LYS cc_start: 0.7599 (pttt) cc_final: 0.7122 (ptpt) REVERT: D 387 GLU cc_start: 0.6988 (tp30) cc_final: 0.6118 (tm-30) REVERT: D 389 GLU cc_start: 0.8179 (tp30) cc_final: 0.7965 (tt0) REVERT: D 444 GLU cc_start: 0.8216 (pm20) cc_final: 0.7954 (mt-10) REVERT: D 445 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7390 (tp30) REVERT: D 490 LYS cc_start: 0.8714 (ttmp) cc_final: 0.8320 (tttp) REVERT: D 626 GLU cc_start: 0.8047 (pt0) cc_final: 0.7492 (pp20) REVERT: D 1132 ARG cc_start: 0.7501 (ttp-170) cc_final: 0.5881 (mmt180) outliers start: 59 outliers final: 31 residues processed: 500 average time/residue: 0.2598 time to fit residues: 204.6699 Evaluate side-chains 457 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 426 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1061 LEU Chi-restraints excluded: chain D residue 1071 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 289 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 349 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 108 optimal weight: 50.0000 chunk 67 optimal weight: 6.9990 chunk 296 optimal weight: 3.9990 chunk 286 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.105205 restraints weight = 43250.597| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.86 r_work: 0.2972 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35932 Z= 0.130 Angle : 0.511 6.513 48360 Z= 0.265 Chirality : 0.040 0.167 5376 Planarity : 0.004 0.039 5992 Dihedral : 10.175 94.497 5548 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 1.56 % Allowed : 9.14 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.13), residues: 4196 helix: 1.51 (0.10), residues: 2588 sheet: -1.07 (0.31), residues: 256 loop : -2.08 (0.15), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 480 TYR 0.010 0.001 TYR D 312 PHE 0.009 0.001 PHE D 584 TRP 0.007 0.001 TRP C 705 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (35924) covalent geometry : angle 0.51040 / 0.26 (48328) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.04986 / 3.31 ( 1892) hydrogen bonds : angle 4.07296 / 2.91 ( 5640) link_BETA1-4 : bond 0.00189 / 0.10 ( 4) link_BETA1-4 : angle 1.61795 / 0.98 ( 12) link_NAG-ASN : bond 0.00118 / 0.06 ( 4) link_NAG-ASN : angle 0.96644 / 0.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 451 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.7826 (mtm) cc_final: 0.7250 (mtp) REVERT: A 220 ASP cc_start: 0.8129 (t70) cc_final: 0.7793 (t0) REVERT: A 276 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7403 (tp30) REVERT: A 310 THR cc_start: 0.8040 (m) cc_final: 0.7826 (p) REVERT: A 383 LYS cc_start: 0.7773 (pttt) cc_final: 0.7306 (ptpt) REVERT: A 387 GLU cc_start: 0.7018 (tp30) cc_final: 0.6224 (tm-30) REVERT: A 389 GLU cc_start: 0.7908 (tt0) cc_final: 0.7500 (tp30) REVERT: A 444 GLU cc_start: 0.8138 (pm20) cc_final: 0.7924 (mt-10) REVERT: A 445 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7289 (tp30) REVERT: A 481 GLU cc_start: 0.8619 (mp0) cc_final: 0.8408 (mp0) REVERT: A 626 GLU cc_start: 0.7843 (pt0) cc_final: 0.7323 (pp20) REVERT: A 1132 ARG cc_start: 0.7442 (ttp-170) cc_final: 0.5834 (mmt180) REVERT: A 1194 ARG cc_start: 0.8232 (mtp85) cc_final: 0.8024 (mmm-85) REVERT: B 197 MET cc_start: 0.7818 (mtm) cc_final: 0.7245 (mtp) REVERT: B 220 ASP cc_start: 0.8135 (t70) cc_final: 0.7797 (t0) REVERT: B 276 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7422 (tp30) REVERT: B 310 THR cc_start: 0.8044 (m) cc_final: 0.7831 (p) REVERT: B 383 LYS cc_start: 0.7574 (pttt) cc_final: 0.7064 (ptpt) REVERT: B 387 GLU cc_start: 0.6968 (tp30) cc_final: 0.6169 (tm-30) REVERT: B 389 GLU cc_start: 0.7918 (tt0) cc_final: 0.7510 (tp30) REVERT: B 444 GLU cc_start: 0.8120 (pm20) cc_final: 0.7900 (mt-10) REVERT: B 445 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7292 (tp30) REVERT: B 479 MET cc_start: 0.8587 (tpp) cc_final: 0.8345 (tpp) REVERT: B 481 GLU cc_start: 0.8586 (mp0) cc_final: 0.8380 (mp0) REVERT: B 490 LYS cc_start: 0.8652 (ttmp) cc_final: 0.8247 (tttp) REVERT: B 1132 ARG cc_start: 0.7435 (ttp-170) cc_final: 0.5824 (mmt180) REVERT: C 197 MET cc_start: 0.7819 (mtm) cc_final: 0.7251 (mtp) REVERT: C 276 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7397 (tp30) REVERT: C 310 THR cc_start: 0.8038 (m) cc_final: 0.7823 (p) REVERT: C 383 LYS cc_start: 0.7578 (pttt) cc_final: 0.6887 (ptpt) REVERT: C 387 GLU cc_start: 0.6966 (tp30) cc_final: 0.6136 (tm-30) REVERT: C 389 GLU cc_start: 0.7925 (tt0) cc_final: 0.7520 (tp30) REVERT: C 444 GLU cc_start: 0.8126 (pm20) cc_final: 0.7908 (mt-10) REVERT: C 445 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7266 (tp30) REVERT: C 479 MET cc_start: 0.8585 (tpp) cc_final: 0.8344 (tpp) REVERT: C 481 GLU cc_start: 0.8597 (mp0) cc_final: 0.8391 (mp0) REVERT: C 490 LYS cc_start: 0.8646 (ttmp) cc_final: 0.8240 (tttp) REVERT: C 1132 ARG cc_start: 0.7486 (ttp-170) cc_final: 0.5856 (mmt180) REVERT: D 197 MET cc_start: 0.7813 (mtm) cc_final: 0.7247 (mtp) REVERT: D 276 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7376 (tp30) REVERT: D 310 THR cc_start: 0.8045 (m) cc_final: 0.7829 (p) REVERT: D 383 LYS cc_start: 0.7646 (pttt) cc_final: 0.7171 (ptpt) REVERT: D 387 GLU cc_start: 0.7062 (tp30) cc_final: 0.6251 (tm-30) REVERT: D 389 GLU cc_start: 0.8059 (tp30) cc_final: 0.7806 (tt0) REVERT: D 444 GLU cc_start: 0.8139 (pm20) cc_final: 0.7922 (mt-10) REVERT: D 445 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7288 (tp30) REVERT: D 481 GLU cc_start: 0.8590 (mp0) cc_final: 0.8387 (mp0) REVERT: D 490 LYS cc_start: 0.8657 (ttmp) cc_final: 0.8248 (tttp) REVERT: D 626 GLU cc_start: 0.7912 (pt0) cc_final: 0.7373 (pp20) REVERT: D 1132 ARG cc_start: 0.7511 (ttp-170) cc_final: 0.5826 (mmt180) outliers start: 56 outliers final: 32 residues processed: 493 average time/residue: 0.2617 time to fit residues: 202.8746 Evaluate side-chains 462 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 430 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1095 ASP Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 528 GLU Chi-restraints excluded: chain D residue 1061 LEU Chi-restraints excluded: chain D residue 1071 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 296 optimal weight: 0.9980 chunk 348 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 126 optimal weight: 0.0670 chunk 2 optimal weight: 40.0000 chunk 195 optimal weight: 0.8980 chunk 293 optimal weight: 1.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.141742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105171 restraints weight = 43353.873| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.80 r_work: 0.2979 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35932 Z= 0.126 Angle : 0.507 6.606 48360 Z= 0.261 Chirality : 0.040 0.144 5376 Planarity : 0.004 0.040 5992 Dihedral : 9.620 93.697 5548 Min Nonbonded Distance : 1.669 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.46 % Favored : 96.45 % Rotamer: Outliers : 1.47 % Allowed : 9.94 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.13), residues: 4196 helix: 1.56 (0.10), residues: 2600 sheet: -1.00 (0.31), residues: 256 loop : -2.00 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 480 TYR 0.021 0.001 TYR D 312 PHE 0.010 0.001 PHE B 584 TRP 0.009 0.001 TRP A 705 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (35924) covalent geometry : angle 0.50641 / 0.26 (48328) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.04826 / 3.20 ( 1892) hydrogen bonds : angle 3.97536 / 2.83 ( 5640) link_BETA1-4 : bond 0.00211 / 0.10 ( 4) link_BETA1-4 : angle 1.65348 / 1.00 ( 12) link_NAG-ASN : bond 0.00052 / 0.03 ( 4) link_NAG-ASN : angle 0.97646 / 0.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 443 time to evaluate : 1.450 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.7808 (mtm) cc_final: 0.7436 (mtp) REVERT: A 220 ASP cc_start: 0.8114 (t70) cc_final: 0.7777 (t0) REVERT: A 276 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7355 (tp30) REVERT: A 310 THR cc_start: 0.7986 (m) cc_final: 0.7778 (p) REVERT: A 383 LYS cc_start: 0.7762 (pttt) cc_final: 0.7208 (ptpt) REVERT: A 387 GLU cc_start: 0.6959 (tp30) cc_final: 0.6672 (mm-30) REVERT: A 389 GLU cc_start: 0.7899 (tt0) cc_final: 0.7503 (tp30) REVERT: A 444 GLU cc_start: 0.8121 (pm20) cc_final: 0.7897 (mt-10) REVERT: A 445 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7299 (tp30) REVERT: A 626 GLU cc_start: 0.7755 (pt0) cc_final: 0.7208 (pp20) REVERT: A 884 PHE cc_start: 0.7746 (t80) cc_final: 0.7538 (t80) REVERT: A 1132 ARG cc_start: 0.7458 (ttp-170) cc_final: 0.5834 (mmt180) REVERT: A 1194 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7992 (mmm-85) REVERT: B 197 MET cc_start: 0.7771 (mtm) cc_final: 0.7405 (mtp) REVERT: B 220 ASP cc_start: 0.8108 (t70) cc_final: 0.7772 (t0) REVERT: B 276 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7369 (tp30) REVERT: B 310 THR cc_start: 0.7994 (m) cc_final: 0.7784 (p) REVERT: B 383 LYS cc_start: 0.7690 (pttt) cc_final: 0.7133 (ptpt) REVERT: B 387 GLU cc_start: 0.6974 (tp30) cc_final: 0.6750 (mm-30) REVERT: B 389 GLU cc_start: 0.7911 (tt0) cc_final: 0.7518 (tp30) REVERT: B 444 GLU cc_start: 0.8114 (pm20) cc_final: 0.7883 (mt-10) REVERT: B 445 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7287 (tp30) REVERT: B 479 MET cc_start: 0.8599 (tpp) cc_final: 0.8364 (tpp) REVERT: B 490 LYS cc_start: 0.8593 (ttmp) cc_final: 0.8180 (tttp) REVERT: B 1132 ARG cc_start: 0.7460 (ttp-170) cc_final: 0.5832 (mmt180) REVERT: B 1194 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7978 (mmm-85) REVERT: C 197 MET cc_start: 0.7769 (mtm) cc_final: 0.7403 (mtp) REVERT: C 276 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7368 (tp30) REVERT: C 310 THR cc_start: 0.8002 (m) cc_final: 0.7790 (p) REVERT: C 383 LYS cc_start: 0.7669 (pttt) cc_final: 0.7128 (ptpt) REVERT: C 387 GLU cc_start: 0.6997 (tp30) cc_final: 0.6188 (tm-30) REVERT: C 389 GLU cc_start: 0.7912 (tt0) cc_final: 0.7521 (tp30) REVERT: C 444 GLU cc_start: 0.8148 (pm20) cc_final: 0.7904 (mt-10) REVERT: C 445 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7255 (tp30) REVERT: C 490 LYS cc_start: 0.8597 (ttmp) cc_final: 0.8182 (tttp) REVERT: C 1132 ARG cc_start: 0.7505 (ttp-170) cc_final: 0.5864 (mmt180) REVERT: C 1194 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7989 (mmm-85) REVERT: D 197 MET cc_start: 0.7801 (mtm) cc_final: 0.7440 (mtp) REVERT: D 276 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7349 (tp30) REVERT: D 310 THR cc_start: 0.8025 (m) cc_final: 0.7817 (p) REVERT: D 383 LYS cc_start: 0.7589 (pttt) cc_final: 0.6971 (ptpt) REVERT: D 387 GLU cc_start: 0.7019 (tp30) cc_final: 0.6199 (tm-30) REVERT: D 389 GLU cc_start: 0.8033 (tp30) cc_final: 0.7789 (tt0) REVERT: D 444 GLU cc_start: 0.8125 (pm20) cc_final: 0.7897 (mt-10) REVERT: D 445 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7296 (tp30) REVERT: D 490 LYS cc_start: 0.8616 (ttmp) cc_final: 0.8197 (tttp) REVERT: D 626 GLU cc_start: 0.7752 (pt0) cc_final: 0.7196 (pp20) REVERT: D 1132 ARG cc_start: 0.7447 (ttp-170) cc_final: 0.5867 (mmt180) outliers start: 53 outliers final: 33 residues processed: 482 average time/residue: 0.2542 time to fit residues: 193.5909 Evaluate side-chains 459 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 426 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 903 LYS Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 752 SER Chi-restraints excluded: chain D residue 1061 LEU Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1095 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 323 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 306 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 387 optimal weight: 5.9990 chunk 296 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.141837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.105319 restraints weight = 43283.577| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.82 r_work: 0.2977 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35932 Z= 0.122 Angle : 0.497 6.789 48360 Z= 0.256 Chirality : 0.039 0.142 5376 Planarity : 0.004 0.041 5992 Dihedral : 9.344 94.000 5544 Min Nonbonded Distance : 1.669 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.19 % Favored : 96.71 % Rotamer: Outliers : 1.81 % Allowed : 10.28 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.13), residues: 4196 helix: 1.64 (0.10), residues: 2596 sheet: -1.04 (0.31), residues: 264 loop : -1.93 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 480 TYR 0.010 0.001 TYR A 312 PHE 0.010 0.001 PHE A 887 TRP 0.008 0.001 TRP C 705 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (35924) covalent geometry : angle 0.49581 / 0.26 (48328) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.04697 / 3.11 ( 1892) hydrogen bonds : angle 3.93050 / 2.80 ( 5640) link_BETA1-4 : bond 0.00309 / 0.15 ( 4) link_BETA1-4 : angle 1.61695 / 0.98 ( 12) link_NAG-ASN : bond 0.00082 / 0.04 ( 4) link_NAG-ASN : angle 0.99419 / 0.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 433 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8159 (pp20) REVERT: A 197 MET cc_start: 0.7788 (mtm) cc_final: 0.7241 (mtp) REVERT: A 220 ASP cc_start: 0.8086 (t70) cc_final: 0.7750 (t0) REVERT: A 223 SER cc_start: 0.7128 (OUTLIER) cc_final: 0.6906 (t) REVERT: A 276 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7371 (tp30) REVERT: A 310 THR cc_start: 0.7986 (m) cc_final: 0.7769 (p) REVERT: A 383 LYS cc_start: 0.7506 (pttt) cc_final: 0.6925 (ptpt) REVERT: A 387 GLU cc_start: 0.6993 (tp30) cc_final: 0.6759 (mm-30) REVERT: A 389 GLU cc_start: 0.7885 (tt0) cc_final: 0.7442 (tp30) REVERT: A 444 GLU cc_start: 0.8103 (pm20) cc_final: 0.7884 (mt-10) REVERT: A 445 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7320 (tp30) REVERT: A 477 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7972 (tm) REVERT: A 626 GLU cc_start: 0.7733 (pt0) cc_final: 0.7206 (pp20) REVERT: A 884 PHE cc_start: 0.7822 (t80) cc_final: 0.7593 (t80) REVERT: A 1132 ARG cc_start: 0.7452 (ttp-170) cc_final: 0.5833 (mmt180) REVERT: A 1194 ARG cc_start: 0.8233 (mtp85) cc_final: 0.8027 (mmm-85) REVERT: B 193 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8167 (pp20) REVERT: B 197 MET cc_start: 0.7769 (mtm) cc_final: 0.7219 (mtp) REVERT: B 220 ASP cc_start: 0.8082 (t70) cc_final: 0.7752 (t0) REVERT: B 223 SER cc_start: 0.7138 (OUTLIER) cc_final: 0.6914 (t) REVERT: B 276 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7369 (tp30) REVERT: B 310 THR cc_start: 0.8006 (m) cc_final: 0.7771 (p) REVERT: B 383 LYS cc_start: 0.7529 (pttt) cc_final: 0.6958 (ptpt) REVERT: B 387 GLU cc_start: 0.6909 (tp30) cc_final: 0.6673 (mm-30) REVERT: B 389 GLU cc_start: 0.7916 (tt0) cc_final: 0.7535 (tp30) REVERT: B 444 GLU cc_start: 0.8087 (pm20) cc_final: 0.7869 (mt-10) REVERT: B 445 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7301 (tp30) REVERT: B 477 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7953 (tm) REVERT: B 490 LYS cc_start: 0.8610 (ttmp) cc_final: 0.8201 (tttp) REVERT: B 884 PHE cc_start: 0.7856 (t80) cc_final: 0.7623 (t80) REVERT: B 1132 ARG cc_start: 0.7423 (ttp-170) cc_final: 0.5851 (mmt180) REVERT: B 1194 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7995 (mmm-85) REVERT: C 193 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8175 (pp20) REVERT: C 197 MET cc_start: 0.7782 (mtm) cc_final: 0.7242 (mtp) REVERT: C 223 SER cc_start: 0.7115 (OUTLIER) cc_final: 0.6902 (t) REVERT: C 276 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7380 (tp30) REVERT: C 310 THR cc_start: 0.8021 (m) cc_final: 0.7815 (p) REVERT: C 383 LYS cc_start: 0.7529 (pttt) cc_final: 0.6800 (ptpt) REVERT: C 387 GLU cc_start: 0.6902 (tp30) cc_final: 0.6678 (mm-30) REVERT: C 389 GLU cc_start: 0.7909 (tt0) cc_final: 0.7462 (tp30) REVERT: C 444 GLU cc_start: 0.8109 (pm20) cc_final: 0.7883 (mt-10) REVERT: C 445 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7280 (tp30) REVERT: C 477 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7935 (tm) REVERT: C 490 LYS cc_start: 0.8610 (ttmp) cc_final: 0.8198 (tttp) REVERT: C 1132 ARG cc_start: 0.7441 (ttp-170) cc_final: 0.5886 (mmt180) REVERT: C 1194 ARG cc_start: 0.8229 (mtp85) cc_final: 0.8010 (mmm-85) REVERT: D 197 MET cc_start: 0.7784 (mtm) cc_final: 0.7236 (mtp) REVERT: D 223 SER cc_start: 0.7122 (OUTLIER) cc_final: 0.6906 (t) REVERT: D 276 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7370 (tp30) REVERT: D 310 THR cc_start: 0.8002 (m) cc_final: 0.7793 (p) REVERT: D 383 LYS cc_start: 0.7636 (pttt) cc_final: 0.6968 (ptpt) REVERT: D 387 GLU cc_start: 0.7042 (tp30) cc_final: 0.6780 (mm-30) REVERT: D 389 GLU cc_start: 0.8035 (tp30) cc_final: 0.7709 (tt0) REVERT: D 444 GLU cc_start: 0.8144 (pm20) cc_final: 0.7909 (mt-10) REVERT: D 445 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7305 (tp30) REVERT: D 477 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7934 (tm) REVERT: D 490 LYS cc_start: 0.8630 (ttmp) cc_final: 0.8214 (tttp) REVERT: D 626 GLU cc_start: 0.7747 (pt0) cc_final: 0.7201 (pp20) REVERT: D 884 PHE cc_start: 0.7854 (t80) cc_final: 0.7620 (t80) REVERT: D 1132 ARG cc_start: 0.7430 (ttp-170) cc_final: 0.5852 (mmt180) outliers start: 65 outliers final: 35 residues processed: 480 average time/residue: 0.2525 time to fit residues: 192.2034 Evaluate side-chains 466 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 420 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 481 GLU Chi-restraints excluded: chain D residue 752 SER Chi-restraints excluded: chain D residue 1061 LEU Chi-restraints excluded: chain D residue 1071 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 124 optimal weight: 0.9990 chunk 349 optimal weight: 5.9990 chunk 301 optimal weight: 0.7980 chunk 165 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 319 optimal weight: 20.0000 chunk 343 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 401 optimal weight: 0.5980 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.141958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.105399 restraints weight = 43505.215| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.79 r_work: 0.2981 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 35932 Z= 0.118 Angle : 0.493 6.821 48360 Z= 0.253 Chirality : 0.039 0.141 5376 Planarity : 0.004 0.041 5992 Dihedral : 9.144 94.058 5544 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.62 % Favored : 96.28 % Rotamer: Outliers : 1.58 % Allowed : 10.58 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.13), residues: 4196 helix: 1.74 (0.10), residues: 2588 sheet: -0.39 (0.33), residues: 232 loop : -1.91 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 344 TYR 0.013 0.001 TYR D 312 PHE 0.008 0.001 PHE D 584 TRP 0.008 0.001 TRP B 705 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (35924) covalent geometry : angle 0.49199 / 0.25 (48328) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.04577 / 3.03 ( 1892) hydrogen bonds : angle 3.87814 / 2.76 ( 5640) link_BETA1-4 : bond 0.00168 / 0.09 ( 4) link_BETA1-4 : angle 1.55652 / 0.94 ( 12) link_NAG-ASN : bond 0.00094 / 0.05 ( 4) link_NAG-ASN : angle 0.96305 / 0.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 426 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.7768 (mtm) cc_final: 0.7212 (mtp) REVERT: A 220 ASP cc_start: 0.8040 (t70) cc_final: 0.7729 (t0) REVERT: A 276 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7380 (tp30) REVERT: A 310 THR cc_start: 0.8013 (m) cc_final: 0.7767 (p) REVERT: A 383 LYS cc_start: 0.7514 (pttt) cc_final: 0.6923 (ptpt) REVERT: A 387 GLU cc_start: 0.6967 (tp30) cc_final: 0.6742 (mm-30) REVERT: A 389 GLU cc_start: 0.7894 (tt0) cc_final: 0.7419 (tp30) REVERT: A 444 GLU cc_start: 0.8084 (pm20) cc_final: 0.7857 (mt-10) REVERT: A 445 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7297 (tp30) REVERT: A 477 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8020 (tm) REVERT: A 626 GLU cc_start: 0.7618 (pt0) cc_final: 0.7115 (pp20) REVERT: A 884 PHE cc_start: 0.7818 (t80) cc_final: 0.7589 (t80) REVERT: A 1132 ARG cc_start: 0.7456 (ttp-170) cc_final: 0.5821 (mmt180) REVERT: A 1194 ARG cc_start: 0.8236 (mtp85) cc_final: 0.8024 (mmm-85) REVERT: B 197 MET cc_start: 0.7714 (mtm) cc_final: 0.7166 (mtp) REVERT: B 220 ASP cc_start: 0.8076 (t70) cc_final: 0.7747 (t0) REVERT: B 276 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7387 (tp30) REVERT: B 310 THR cc_start: 0.8014 (m) cc_final: 0.7769 (p) REVERT: B 383 LYS cc_start: 0.7543 (pttt) cc_final: 0.6960 (ptpt) REVERT: B 387 GLU cc_start: 0.6883 (tp30) cc_final: 0.6655 (mm-30) REVERT: B 389 GLU cc_start: 0.7829 (tt0) cc_final: 0.7421 (tp30) REVERT: B 444 GLU cc_start: 0.8087 (pm20) cc_final: 0.7879 (mt-10) REVERT: B 445 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7298 (tp30) REVERT: B 477 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7968 (tm) REVERT: B 490 LYS cc_start: 0.8611 (ttmp) cc_final: 0.8200 (tttp) REVERT: B 884 PHE cc_start: 0.7823 (t80) cc_final: 0.7594 (t80) REVERT: B 1132 ARG cc_start: 0.7519 (ttp-170) cc_final: 0.5920 (mmt180) REVERT: B 1194 ARG cc_start: 0.8221 (mtp85) cc_final: 0.7998 (mmm-85) REVERT: C 197 MET cc_start: 0.7730 (mtm) cc_final: 0.7196 (mtp) REVERT: C 223 SER cc_start: 0.7162 (OUTLIER) cc_final: 0.6949 (t) REVERT: C 276 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7401 (tp30) REVERT: C 310 THR cc_start: 0.7933 (m) cc_final: 0.7722 (p) REVERT: C 383 LYS cc_start: 0.7533 (pttt) cc_final: 0.6760 (ptpt) REVERT: C 387 GLU cc_start: 0.6970 (tp30) cc_final: 0.6747 (mm-30) REVERT: C 389 GLU cc_start: 0.7911 (tt0) cc_final: 0.7426 (tp30) REVERT: C 444 GLU cc_start: 0.8083 (pm20) cc_final: 0.7859 (mt-10) REVERT: C 445 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7287 (tp30) REVERT: C 477 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8023 (tm) REVERT: C 490 LYS cc_start: 0.8608 (ttmp) cc_final: 0.8196 (tttp) REVERT: C 1132 ARG cc_start: 0.7474 (ttp-170) cc_final: 0.5915 (mmt180) REVERT: C 1194 ARG cc_start: 0.8229 (mtp85) cc_final: 0.8004 (mmm-85) REVERT: D 197 MET cc_start: 0.7766 (mtm) cc_final: 0.7407 (mtp) REVERT: D 223 SER cc_start: 0.7163 (OUTLIER) cc_final: 0.6947 (t) REVERT: D 276 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7388 (tp30) REVERT: D 310 THR cc_start: 0.7964 (m) cc_final: 0.7744 (p) REVERT: D 383 LYS cc_start: 0.7529 (pttt) cc_final: 0.6741 (ptpt) REVERT: D 387 GLU cc_start: 0.6952 (tp30) cc_final: 0.6636 (mm-30) REVERT: D 389 GLU cc_start: 0.8028 (tp30) cc_final: 0.7704 (tt0) REVERT: D 444 GLU cc_start: 0.8108 (pm20) cc_final: 0.7896 (mt-10) REVERT: D 445 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7299 (tp30) REVERT: D 477 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8029 (tm) REVERT: D 490 LYS cc_start: 0.8630 (ttmp) cc_final: 0.8213 (tttp) REVERT: D 626 GLU cc_start: 0.7721 (pt0) cc_final: 0.7188 (pp20) REVERT: D 1132 ARG cc_start: 0.7475 (ttp-170) cc_final: 0.5898 (mmt180) outliers start: 57 outliers final: 38 residues processed: 469 average time/residue: 0.2437 time to fit residues: 181.4070 Evaluate side-chains 454 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 410 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 481 GLU Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1061 LEU Chi-restraints excluded: chain D residue 1071 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 69 optimal weight: 4.9990 chunk 204 optimal weight: 0.3980 chunk 395 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 366 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 300 optimal weight: 0.6980 chunk 338 optimal weight: 0.0270 chunk 293 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.141697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.105040 restraints weight = 43636.961| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.85 r_work: 0.2969 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35932 Z= 0.123 Angle : 0.497 7.000 48360 Z= 0.255 Chirality : 0.039 0.142 5376 Planarity : 0.004 0.042 5992 Dihedral : 9.050 93.811 5544 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 1.44 % Allowed : 10.56 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.13), residues: 4196 helix: 1.76 (0.10), residues: 2588 sheet: -0.35 (0.33), residues: 232 loop : -1.91 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 480 TYR 0.014 0.001 TYR D 312 PHE 0.009 0.001 PHE D 887 TRP 0.008 0.001 TRP A 705 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (35924) covalent geometry : angle 0.49600 / 0.25 (48328) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.04676 / 3.10 ( 1892) hydrogen bonds : angle 3.87646 / 2.76 ( 5640) link_BETA1-4 : bond 0.00156 / 0.08 ( 4) link_BETA1-4 : angle 1.57139 / 0.95 ( 12) link_NAG-ASN : bond 0.00060 / 0.03 ( 4) link_NAG-ASN : angle 1.02205 / 0.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 419 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.8286 (tpp) cc_final: 0.8044 (tpp) REVERT: A 197 MET cc_start: 0.7803 (mtm) cc_final: 0.7421 (mtp) REVERT: A 220 ASP cc_start: 0.8036 (t70) cc_final: 0.7727 (t0) REVERT: A 276 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7328 (tp30) REVERT: A 310 THR cc_start: 0.7993 (m) cc_final: 0.7748 (p) REVERT: A 383 LYS cc_start: 0.7498 (pttt) cc_final: 0.6895 (ptpt) REVERT: A 387 GLU cc_start: 0.6940 (tp30) cc_final: 0.6716 (mm-30) REVERT: A 389 GLU cc_start: 0.7882 (tt0) cc_final: 0.7394 (tp30) REVERT: A 444 GLU cc_start: 0.8082 (pm20) cc_final: 0.7836 (mt-10) REVERT: A 445 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7281 (tp30) REVERT: A 477 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8040 (tm) REVERT: A 626 GLU cc_start: 0.7592 (pt0) cc_final: 0.7084 (pp20) REVERT: A 1132 ARG cc_start: 0.7462 (ttp-170) cc_final: 0.5889 (mmt180) REVERT: B 158 MET cc_start: 0.8269 (tpp) cc_final: 0.8030 (tpp) REVERT: B 197 MET cc_start: 0.7742 (mtm) cc_final: 0.7334 (mtp) REVERT: B 220 ASP cc_start: 0.8041 (t70) cc_final: 0.7732 (t0) REVERT: B 276 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7328 (tp30) REVERT: B 310 THR cc_start: 0.7965 (m) cc_final: 0.7732 (p) REVERT: B 383 LYS cc_start: 0.7509 (pttt) cc_final: 0.6907 (ptpt) REVERT: B 387 GLU cc_start: 0.6896 (tp30) cc_final: 0.6678 (mm-30) REVERT: B 389 GLU cc_start: 0.7890 (tt0) cc_final: 0.7416 (tp30) REVERT: B 444 GLU cc_start: 0.8065 (pm20) cc_final: 0.7836 (mt-10) REVERT: B 445 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7294 (tp30) REVERT: B 477 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8042 (tm) REVERT: B 490 LYS cc_start: 0.8590 (ttmp) cc_final: 0.8179 (tttp) REVERT: B 1132 ARG cc_start: 0.7510 (ttp-170) cc_final: 0.5920 (mmt180) REVERT: B 1194 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7985 (mmm-85) REVERT: C 197 MET cc_start: 0.7741 (mtm) cc_final: 0.7343 (mtp) REVERT: C 223 SER cc_start: 0.7157 (OUTLIER) cc_final: 0.6938 (t) REVERT: C 276 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7368 (tp30) REVERT: C 310 THR cc_start: 0.7976 (m) cc_final: 0.7755 (p) REVERT: C 383 LYS cc_start: 0.7484 (pttt) cc_final: 0.6707 (ptpt) REVERT: C 387 GLU cc_start: 0.6939 (tp30) cc_final: 0.6692 (mm-30) REVERT: C 389 GLU cc_start: 0.7897 (tt0) cc_final: 0.7424 (tp30) REVERT: C 444 GLU cc_start: 0.8074 (pm20) cc_final: 0.7840 (mt-10) REVERT: C 445 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7255 (tp30) REVERT: C 477 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8021 (tm) REVERT: C 490 LYS cc_start: 0.8589 (ttmp) cc_final: 0.8177 (tttp) REVERT: C 1132 ARG cc_start: 0.7466 (ttp-170) cc_final: 0.5916 (mmt180) REVERT: C 1194 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7988 (mmm-85) REVERT: D 197 MET cc_start: 0.7776 (mtm) cc_final: 0.7396 (mtp) REVERT: D 223 SER cc_start: 0.7167 (OUTLIER) cc_final: 0.6944 (t) REVERT: D 276 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7391 (tp30) REVERT: D 310 THR cc_start: 0.7962 (m) cc_final: 0.7741 (p) REVERT: D 383 LYS cc_start: 0.7641 (pttt) cc_final: 0.6862 (ptpt) REVERT: D 387 GLU cc_start: 0.6932 (tp30) cc_final: 0.6606 (mm-30) REVERT: D 389 GLU cc_start: 0.8020 (tp30) cc_final: 0.7684 (tt0) REVERT: D 444 GLU cc_start: 0.8077 (pm20) cc_final: 0.7850 (mt-10) REVERT: D 445 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7286 (tp30) REVERT: D 477 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8030 (tm) REVERT: D 490 LYS cc_start: 0.8607 (ttmp) cc_final: 0.8188 (tttp) REVERT: D 626 GLU cc_start: 0.7711 (pt0) cc_final: 0.7172 (pp20) REVERT: D 1132 ARG cc_start: 0.7465 (ttp-170) cc_final: 0.5898 (mmt180) outliers start: 52 outliers final: 37 residues processed: 456 average time/residue: 0.2592 time to fit residues: 187.0327 Evaluate side-chains 460 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 417 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 819 MET Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 481 GLU Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1061 LEU Chi-restraints excluded: chain D residue 1071 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 182 optimal weight: 0.1980 chunk 379 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 234 optimal weight: 5.9990 chunk 377 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 230 optimal weight: 0.7980 chunk 279 optimal weight: 6.9990 chunk 391 optimal weight: 4.9990 chunk 295 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.102563 restraints weight = 43356.855| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.85 r_work: 0.2933 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35932 Z= 0.158 Angle : 0.543 8.026 48360 Z= 0.276 Chirality : 0.041 0.153 5376 Planarity : 0.004 0.043 5992 Dihedral : 9.303 91.806 5544 Min Nonbonded Distance : 1.635 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 1.33 % Allowed : 10.83 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.13), residues: 4196 helix: 1.59 (0.10), residues: 2612 sheet: -0.36 (0.34), residues: 232 loop : -1.97 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 480 TYR 0.017 0.001 TYR D 312 PHE 0.013 0.001 PHE A 887 TRP 0.009 0.001 TRP C 885 HIS 0.004 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (35924) covalent geometry : angle 0.54175 / 0.28 (48328) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.05364 / 3.57 ( 1892) hydrogen bonds : angle 3.98904 / 2.84 ( 5640) link_BETA1-4 : bond 0.00026 / 0.01 ( 4) link_BETA1-4 : angle 1.71503 / 1.04 ( 12) link_NAG-ASN : bond 0.00166 / 0.08 ( 4) link_NAG-ASN : angle 1.37156 / 0.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 416 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.7862 (mtm) cc_final: 0.7475 (mtp) REVERT: A 220 ASP cc_start: 0.8127 (t70) cc_final: 0.7800 (t0) REVERT: A 276 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7335 (tp30) REVERT: A 310 THR cc_start: 0.8014 (m) cc_final: 0.7784 (p) REVERT: A 377 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7863 (mmmt) REVERT: A 383 LYS cc_start: 0.7540 (pttt) cc_final: 0.6958 (ptpt) REVERT: A 444 GLU cc_start: 0.8075 (pm20) cc_final: 0.7815 (mt-10) REVERT: A 445 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7333 (tp30) REVERT: A 477 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8169 (tm) REVERT: A 626 GLU cc_start: 0.7686 (pt0) cc_final: 0.7149 (pp20) REVERT: A 1132 ARG cc_start: 0.7587 (ttp-170) cc_final: 0.5966 (mmt180) REVERT: B 197 MET cc_start: 0.7834 (mtm) cc_final: 0.7444 (mtp) REVERT: B 220 ASP cc_start: 0.8119 (t70) cc_final: 0.7797 (t0) REVERT: B 276 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7332 (tp30) REVERT: B 310 THR cc_start: 0.8022 (m) cc_final: 0.7796 (p) REVERT: B 383 LYS cc_start: 0.7556 (pttt) cc_final: 0.6832 (ptpt) REVERT: B 444 GLU cc_start: 0.8061 (pm20) cc_final: 0.7816 (mt-10) REVERT: B 445 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7365 (tp30) REVERT: B 477 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8138 (tm) REVERT: B 490 LYS cc_start: 0.8587 (ttmp) cc_final: 0.8233 (tttp) REVERT: B 1132 ARG cc_start: 0.7613 (ttp-170) cc_final: 0.5990 (mmt180) REVERT: C 197 MET cc_start: 0.7849 (mtm) cc_final: 0.7464 (mtp) REVERT: C 223 SER cc_start: 0.7187 (OUTLIER) cc_final: 0.6925 (t) REVERT: C 276 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7426 (tp30) REVERT: C 383 LYS cc_start: 0.7539 (pttt) cc_final: 0.6739 (ptpt) REVERT: C 387 GLU cc_start: 0.6967 (tp30) cc_final: 0.6720 (mm-30) REVERT: C 444 GLU cc_start: 0.8064 (pm20) cc_final: 0.7820 (mt-10) REVERT: C 445 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7331 (tp30) REVERT: C 477 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8144 (tm) REVERT: C 490 LYS cc_start: 0.8615 (ttmp) cc_final: 0.8250 (tttp) REVERT: C 1132 ARG cc_start: 0.7656 (ttp-170) cc_final: 0.5981 (mmt180) REVERT: D 197 MET cc_start: 0.7848 (mtm) cc_final: 0.7469 (mtp) REVERT: D 276 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7420 (tp30) REVERT: D 383 LYS cc_start: 0.7725 (pttt) cc_final: 0.6893 (ptpt) REVERT: D 387 GLU cc_start: 0.6887 (tp30) cc_final: 0.6654 (mm-30) REVERT: D 389 GLU cc_start: 0.8034 (tp30) cc_final: 0.7699 (tt0) REVERT: D 444 GLU cc_start: 0.8071 (pm20) cc_final: 0.7830 (mt-10) REVERT: D 445 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7349 (tp30) REVERT: D 477 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8162 (tm) REVERT: D 490 LYS cc_start: 0.8621 (ttmp) cc_final: 0.8255 (tttp) REVERT: D 626 GLU cc_start: 0.7827 (pt0) cc_final: 0.7289 (pp20) REVERT: D 1132 ARG cc_start: 0.7597 (ttp-170) cc_final: 0.5984 (mmt180) outliers start: 48 outliers final: 36 residues processed: 455 average time/residue: 0.2552 time to fit residues: 183.8826 Evaluate side-chains 453 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 412 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 481 GLU Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 752 SER Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1061 LEU Chi-restraints excluded: chain D residue 1071 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 229 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 408 optimal weight: 0.9980 chunk 336 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 355 optimal weight: 0.8980 chunk 364 optimal weight: 0.0020 chunk 372 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.103009 restraints weight = 43639.672| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.84 r_work: 0.2948 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35932 Z= 0.145 Angle : 0.525 8.056 48360 Z= 0.268 Chirality : 0.040 0.151 5376 Planarity : 0.004 0.043 5992 Dihedral : 9.210 92.885 5544 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.65 % Favored : 96.26 % Rotamer: Outliers : 1.22 % Allowed : 11.06 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.13), residues: 4196 helix: 1.63 (0.10), residues: 2612 sheet: -0.45 (0.34), residues: 236 loop : -1.92 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 480 TYR 0.013 0.001 TYR D 312 PHE 0.011 0.001 PHE C 584 TRP 0.009 0.001 TRP C 705 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (35924) covalent geometry : angle 0.52450 / 0.27 (48328) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.05130 / 3.41 ( 1892) hydrogen bonds : angle 3.95989 / 2.82 ( 5640) link_BETA1-4 : bond 0.00050 / 0.02 ( 4) link_BETA1-4 : angle 1.63132 / 0.98 ( 12) link_NAG-ASN : bond 0.00049 / 0.02 ( 4) link_NAG-ASN : angle 1.22594 / 0.74 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 414 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.7838 (mtm) cc_final: 0.7500 (mtp) REVERT: A 220 ASP cc_start: 0.8103 (t70) cc_final: 0.7764 (t0) REVERT: A 276 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7350 (tp30) REVERT: A 310 THR cc_start: 0.8018 (m) cc_final: 0.7785 (p) REVERT: A 377 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7868 (mmmt) REVERT: A 383 LYS cc_start: 0.7540 (pttt) cc_final: 0.6999 (ptpt) REVERT: A 444 GLU cc_start: 0.8079 (pm20) cc_final: 0.7813 (mt-10) REVERT: A 445 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7344 (tp30) REVERT: A 477 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8156 (tm) REVERT: A 626 GLU cc_start: 0.7664 (pt0) cc_final: 0.7134 (pp20) REVERT: A 1132 ARG cc_start: 0.7583 (ttp-170) cc_final: 0.5959 (mmt180) REVERT: A 1194 ARG cc_start: 0.7906 (mmm-85) cc_final: 0.7694 (mtp85) REVERT: B 197 MET cc_start: 0.7825 (mtm) cc_final: 0.7491 (mtp) REVERT: B 220 ASP cc_start: 0.8119 (t70) cc_final: 0.7787 (t0) REVERT: B 276 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7353 (tp30) REVERT: B 310 THR cc_start: 0.8022 (m) cc_final: 0.7791 (p) REVERT: B 383 LYS cc_start: 0.7562 (pttt) cc_final: 0.6879 (ptpt) REVERT: B 389 GLU cc_start: 0.8051 (tt0) cc_final: 0.7534 (tp30) REVERT: B 444 GLU cc_start: 0.8060 (pm20) cc_final: 0.7821 (mt-10) REVERT: B 445 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7345 (tp30) REVERT: B 477 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8136 (tm) REVERT: B 490 LYS cc_start: 0.8606 (ttmp) cc_final: 0.8250 (tttp) REVERT: B 1132 ARG cc_start: 0.7606 (ttp-170) cc_final: 0.5981 (mmt180) REVERT: C 197 MET cc_start: 0.7838 (mtm) cc_final: 0.7507 (mtp) REVERT: C 276 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7410 (tp30) REVERT: C 383 LYS cc_start: 0.7535 (pttt) cc_final: 0.6732 (ptpt) REVERT: C 387 GLU cc_start: 0.6920 (tp30) cc_final: 0.6712 (mm-30) REVERT: C 389 GLU cc_start: 0.7963 (tt0) cc_final: 0.7412 (tp30) REVERT: C 444 GLU cc_start: 0.8066 (pm20) cc_final: 0.7823 (mt-10) REVERT: C 445 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7332 (tp30) REVERT: C 477 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8134 (tm) REVERT: C 490 LYS cc_start: 0.8605 (ttmp) cc_final: 0.8210 (tttp) REVERT: C 1132 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.5972 (mmt180) REVERT: D 197 MET cc_start: 0.7841 (mtm) cc_final: 0.7529 (mtp) REVERT: D 276 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7428 (tp30) REVERT: D 383 LYS cc_start: 0.7707 (pttt) cc_final: 0.6877 (ptpt) REVERT: D 387 GLU cc_start: 0.6870 (tp30) cc_final: 0.6644 (mm-30) REVERT: D 389 GLU cc_start: 0.8022 (tp30) cc_final: 0.7684 (tt0) REVERT: D 444 GLU cc_start: 0.8077 (pm20) cc_final: 0.7842 (mt-10) REVERT: D 445 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7349 (tp30) REVERT: D 477 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8148 (tm) REVERT: D 490 LYS cc_start: 0.8630 (ttmp) cc_final: 0.8267 (tttp) REVERT: D 626 GLU cc_start: 0.7833 (pt0) cc_final: 0.7297 (pp20) REVERT: D 1132 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.5969 (mmt180) outliers start: 44 outliers final: 39 residues processed: 447 average time/residue: 0.2611 time to fit residues: 184.1184 Evaluate side-chains 456 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 413 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 481 GLU Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 752 SER Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1061 LEU Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1095 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 32 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 267 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 242 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.102678 restraints weight = 43312.790| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.79 r_work: 0.2939 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35932 Z= 0.155 Angle : 0.538 8.228 48360 Z= 0.273 Chirality : 0.041 0.152 5376 Planarity : 0.004 0.044 5992 Dihedral : 9.265 92.087 5544 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 1.25 % Allowed : 10.83 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.13), residues: 4196 helix: 1.59 (0.10), residues: 2616 sheet: -0.48 (0.34), residues: 236 loop : -1.95 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 480 TYR 0.014 0.001 TYR D 312 PHE 0.012 0.001 PHE C 584 TRP 0.009 0.001 TRP C 885 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 (35924) covalent geometry : angle 0.53667 / 0.27 (48328) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.05288 / 3.51 ( 1892) hydrogen bonds : angle 3.98084 / 2.83 ( 5640) link_BETA1-4 : bond 0.00055 / 0.03 ( 4) link_BETA1-4 : angle 1.71620 / 1.04 ( 12) link_NAG-ASN : bond 0.00077 / 0.04 ( 4) link_NAG-ASN : angle 1.28196 / 0.78 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9765.91 seconds wall clock time: 167 minutes 31.76 seconds (10051.76 seconds total)