Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 14 21:58:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqv_23489/07_2023/7lqv_23489.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqv_23489/07_2023/7lqv_23489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqv_23489/07_2023/7lqv_23489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqv_23489/07_2023/7lqv_23489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqv_23489/07_2023/7lqv_23489.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqv_23489/07_2023/7lqv_23489.pdb" } resolution = 3.25 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 19854 2.51 5 N 5185 2.21 5 O 6091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "B TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1107": "NH1" <-> "NH2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "L TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 30": "OD1" <-> "OD2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 30": "OD1" <-> "OD2" Residue "X ASP 51": "OD1" <-> "OD2" Residue "X GLU 60": "OE1" <-> "OE2" Residue "X PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 81": "OE1" <-> "OE2" Residue "Y TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 101": "OD1" <-> "OD2" Residue "Z TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 60": "OE1" <-> "OE2" Residue "Z PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 31274 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8535 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 55, 'TRANS': 1036} Chain breaks: 4 Chain: "B" Number of atoms: 8681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8681 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 55, 'TRANS': 1056} Chain breaks: 3 Chain: "C" Number of atoms: 8500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8500 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 55, 'TRANS': 1031} Chain breaks: 4 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 941 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 784 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "W" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 941 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "X" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 775 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain breaks: 1 Chain: "Y" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 941 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "Z" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 784 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.47, per 1000 atoms: 0.43 Number of scatterers: 31274 At special positions: 0 Unit cell: (198.904, 186.208, 203.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 6091 8.00 N 5185 7.00 C 19854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1306 " - " ASN A 603 " " NAG A1309 " - " ASN A 709 " " NAG B1303 " - " ASN B 331 " " NAG B1306 " - " ASN B 657 " Time building additional restraints: 10.74 Conformation dependent library (CDL) restraints added in 4.4 seconds 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7408 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 65 sheets defined 20.8% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.855A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 625 removed outlier: 3.681A pdb=" N HIS A 625 " --> pdb=" O PRO A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 629 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.602A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 removed outlier: 3.769A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 854' Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.786A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.254A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.577A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.174A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 removed outlier: 3.666A pdb=" N LEU A1145 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.839A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.637A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 removed outlier: 3.823A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 631 through 636' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.598A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.850A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.519A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 840 removed outlier: 3.764A pdb=" N ASP B 839 " --> pdb=" O LYS B 835 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 removed outlier: 3.506A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 850 through 855' Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.891A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.386A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.615A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.283A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.077A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.641A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 368' Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.031A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.980A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 624 removed outlier: 3.614A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.934A pdb=" N VAL C 635 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR C 636 " --> pdb=" O TRP C 633 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.781A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.978A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.566A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 856 removed outlier: 3.712A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 853 through 856' Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.859A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.318A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.524A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.401A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.964A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.774A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 4.037A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'H' and resid 100B through 100F removed outlier: 3.515A pdb=" N TYR H 100F" --> pdb=" O GLU H 100C" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.753A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 100B through 100F Processing helix chain 'X' and resid 79 through 83 removed outlier: 3.751A pdb=" N GLU X 83 " --> pdb=" O ALA X 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100B through 100F Processing helix chain 'Z' and resid 79 through 83 removed outlier: 3.607A pdb=" N GLU Z 83 " --> pdb=" O ALA Z 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.785A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.785A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.549A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.631A pdb=" N HIS A 69 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.148A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.147A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 224 through 229 removed outlier: 5.446A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.427A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.548A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.615A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.553A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 587 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.791A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.328A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.515A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.725A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.562A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.629A pdb=" N HIS B 69 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.945A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.997A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.408A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.508A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 374 through 379 removed outlier: 4.543A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.531A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.331A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.619A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.297A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.528A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.410A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.527A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 68 through 69 removed outlier: 3.646A pdb=" N HIS C 69 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG C 78 " --> pdb=" O HIS C 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.214A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.794A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN C 125 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 225 through 229 removed outlier: 5.384A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.653A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.019A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.019A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 653 through 655 removed outlier: 5.953A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.721A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.297A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.853A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.717A pdb=" N VAL H 20 " --> pdb=" O MET H 80 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS H 22 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP H 72 " --> pdb=" O THR H 77 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.643A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N SER H 112 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AF8, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.914A pdb=" N ALA L 90 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL L 97 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.626A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 5 through 6 removed outlier: 3.975A pdb=" N VAL W 20 " --> pdb=" O MET W 80 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET W 80 " --> pdb=" O VAL W 20 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA W 78 " --> pdb=" O CYS W 22 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR W 77 " --> pdb=" O ASP W 72 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP W 72 " --> pdb=" O THR W 77 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 10 through 13 removed outlier: 6.604A pdb=" N GLU W 10 " --> pdb=" O THR W 110 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N SER W 112 " --> pdb=" O GLU W 10 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS W 12 " --> pdb=" O SER W 112 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR W 90 " --> pdb=" O THR W 107 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE W 34 " --> pdb=" O ARG W 50 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG W 50 " --> pdb=" O ILE W 34 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TRP W 36 " --> pdb=" O MET W 48 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET W 48 " --> pdb=" O TRP W 36 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 9 through 12 Processing sheet with id=AG4, first strand: chain 'X' and resid 9 through 12 removed outlier: 3.994A pdb=" N ALA X 90 " --> pdb=" O VAL X 97 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL X 97 " --> pdb=" O ALA X 90 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 19 through 24 removed outlier: 3.543A pdb=" N ALA X 19 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA X 71 " --> pdb=" O CYS X 23 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 5 through 6 removed outlier: 3.851A pdb=" N VAL Y 20 " --> pdb=" O MET Y 80 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET Y 80 " --> pdb=" O VAL Y 20 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA Y 78 " --> pdb=" O CYS Y 22 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR Y 77 " --> pdb=" O ASP Y 72 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP Y 72 " --> pdb=" O THR Y 77 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.615A pdb=" N GLU Y 10 " --> pdb=" O THR Y 110 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SER Y 112 " --> pdb=" O GLU Y 10 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS Y 12 " --> pdb=" O SER Y 112 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR Y 90 " --> pdb=" O THR Y 107 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE Y 34 " --> pdb=" O ARG Y 50 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ARG Y 50 " --> pdb=" O ILE Y 34 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TRP Y 36 " --> pdb=" O MET Y 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.615A pdb=" N GLU Y 10 " --> pdb=" O THR Y 110 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SER Y 112 " --> pdb=" O GLU Y 10 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS Y 12 " --> pdb=" O SER Y 112 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR Y 90 " --> pdb=" O THR Y 107 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL Y 102 " --> pdb=" O SER Y 94 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 9 through 13 Processing sheet with id=AH1, first strand: chain 'Z' and resid 9 through 13 removed outlier: 4.026A pdb=" N ALA Z 90 " --> pdb=" O VAL Z 97 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL Z 97 " --> pdb=" O ALA Z 90 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 19 through 24 removed outlier: 3.578A pdb=" N ALA Z 19 " --> pdb=" O ILE Z 75 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA Z 71 " --> pdb=" O CYS Z 23 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 2817 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: 13.58 Time building geometry restraints manager: 11.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7222 1.33 - 1.45: 7464 1.45 - 1.58: 17108 1.58 - 1.70: 1 1.70 - 1.83: 186 Bond restraints: 31981 Sorted by residual: bond pdb=" CA SER A 816 " pdb=" CB SER A 816 " ideal model delta sigma weight residual 1.530 1.465 0.065 1.52e-02 4.33e+03 1.84e+01 bond pdb=" CB ASN A1134 " pdb=" CG ASN A1134 " ideal model delta sigma weight residual 1.516 1.582 -0.066 2.50e-02 1.60e+03 6.90e+00 bond pdb=" N ASP A 53 " pdb=" CA ASP A 53 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.16e-02 7.43e+03 5.70e+00 bond pdb=" C LEU A 54 " pdb=" O LEU A 54 " ideal model delta sigma weight residual 1.234 1.207 0.028 1.19e-02 7.06e+03 5.38e+00 bond pdb=" N LYS A 814 " pdb=" CA LYS A 814 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.12e-02 7.97e+03 5.33e+00 ... (remaining 31976 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.31: 802 106.31 - 113.24: 17391 113.24 - 120.18: 10779 120.18 - 127.11: 14233 127.11 - 134.04: 327 Bond angle restraints: 43532 Sorted by residual: angle pdb=" CA ARG A 815 " pdb=" C ARG A 815 " pdb=" O ARG A 815 " ideal model delta sigma weight residual 121.88 116.39 5.49 1.13e+00 7.83e-01 2.36e+01 angle pdb=" CA LEU A 54 " pdb=" C LEU A 54 " pdb=" O LEU A 54 " ideal model delta sigma weight residual 121.19 116.49 4.70 1.10e+00 8.26e-01 1.83e+01 angle pdb=" N ALA A 522 " pdb=" CA ALA A 522 " pdb=" C ALA A 522 " ideal model delta sigma weight residual 107.73 113.94 -6.21 1.61e+00 3.86e-01 1.49e+01 angle pdb=" CA ASP A 53 " pdb=" C ASP A 53 " pdb=" O ASP A 53 " ideal model delta sigma weight residual 121.38 117.51 3.87 1.06e+00 8.90e-01 1.34e+01 angle pdb=" C THR A 51 " pdb=" CA THR A 51 " pdb=" CB THR A 51 " ideal model delta sigma weight residual 110.62 105.31 5.31 1.51e+00 4.39e-01 1.24e+01 ... (remaining 43527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17114 17.96 - 35.93: 1375 35.93 - 53.89: 251 53.89 - 71.85: 48 71.85 - 89.81: 32 Dihedral angle restraints: 18820 sinusoidal: 7272 harmonic: 11548 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -167.85 81.85 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 13.70 79.30 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 26.68 66.32 1 1.00e+01 1.00e-02 5.74e+01 ... (remaining 18817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3782 0.040 - 0.080: 729 0.080 - 0.120: 414 0.120 - 0.160: 60 0.160 - 0.200: 8 Chirality restraints: 4993 Sorted by residual: chirality pdb=" CA THR A 51 " pdb=" N THR A 51 " pdb=" C THR A 51 " pdb=" CB THR A 51 " both_signs ideal model delta sigma weight residual False 2.53 2.73 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA LEU A 821 " pdb=" N LEU A 821 " pdb=" C LEU A 821 " pdb=" CB LEU A 821 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.91e-01 ... (remaining 4990 not shown) Planarity restraints: 5594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A1106 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" CD GLN A1106 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLN A1106 " 0.017 2.00e-02 2.50e+03 pdb=" NE2 GLN A1106 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C1089 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO C1090 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C1090 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C1090 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 54 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C LEU A 54 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 54 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A 55 " -0.011 2.00e-02 2.50e+03 ... (remaining 5591 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 363 2.60 - 3.17: 27614 3.17 - 3.75: 45904 3.75 - 4.32: 64638 4.32 - 4.90: 107725 Nonbonded interactions: 246244 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" O ALA A 522 " model vdw 2.020 2.440 nonbonded pdb=" O ALA A 879 " pdb=" OG1 THR A 883 " model vdw 2.040 2.440 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.067 2.440 nonbonded pdb=" OG SER B 816 " pdb=" OE1 GLU B 819 " model vdw 2.089 2.440 nonbonded pdb=" OE2 GLU C 654 " pdb=" OG SER C 691 " model vdw 2.098 2.440 ... (remaining 246239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 827 or resid 853 through 1147 or resid 1301 thr \ ough 1308)) selection = (chain 'B' and (resid 14 through 827 or resid 853 through 1147 or resid 1301 thr \ ough 1308)) selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = (chain 'L' and (resid 2 through 49 or resid 51 through 106A)) selection = chain 'X' selection = (chain 'Z' and (resid 2 through 49 or resid 51 through 106A)) } 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.300 Check model and map are aligned: 0.480 Set scattering table: 0.300 Process input model: 72.400 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.170 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 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 : 0.003 0.066 31981 Z= 0.209 Angle : 0.556 6.633 43532 Z= 0.297 Chirality : 0.043 0.200 4993 Planarity : 0.003 0.049 5590 Dihedral : 13.533 89.814 11265 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.62 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3938 helix: 1.82 (0.22), residues: 607 sheet: 0.08 (0.18), residues: 809 loop : -0.96 (0.13), residues: 2522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 190 average time/residue: 0.4048 time to fit residues: 130.4992 Evaluate side-chains 134 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 3.380 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6613 time to fit residues: 5.6092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 332 optimal weight: 30.0000 chunk 298 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 chunk 308 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 187 optimal weight: 0.2980 chunk 229 optimal weight: 10.0000 chunk 357 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1134 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1058 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 ASN C 935 GLN C1002 GLN C1005 GLN H 1 GLN H 39 GLN H 96 GLN L 38 GLN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 GLN X 37 GLN X 38 GLN Y 39 GLN Z 38 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 31981 Z= 0.343 Angle : 0.620 8.814 43532 Z= 0.323 Chirality : 0.046 0.303 4993 Planarity : 0.004 0.049 5590 Dihedral : 4.167 35.066 4270 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.48 % Favored : 93.50 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 3938 helix: 1.53 (0.21), residues: 632 sheet: 0.01 (0.17), residues: 832 loop : -1.09 (0.13), residues: 2474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 3.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 174 average time/residue: 0.3720 time to fit residues: 114.0030 Evaluate side-chains 134 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 3.337 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2927 time to fit residues: 8.9563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 198 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 358 optimal weight: 9.9990 chunk 387 optimal weight: 8.9990 chunk 319 optimal weight: 0.7980 chunk 355 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 287 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 613 GLN A 853 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN B1002 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 804 GLN C1005 GLN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 89 GLN Z 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 31981 Z= 0.244 Angle : 0.545 9.273 43532 Z= 0.285 Chirality : 0.044 0.297 4993 Planarity : 0.004 0.051 5590 Dihedral : 4.095 35.440 4270 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 3938 helix: 1.46 (0.21), residues: 637 sheet: -0.06 (0.17), residues: 859 loop : -1.12 (0.13), residues: 2442 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 177 average time/residue: 0.3833 time to fit residues: 120.1635 Evaluate side-chains 148 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 3.491 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2825 time to fit residues: 13.0492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 354 optimal weight: 10.0000 chunk 269 optimal weight: 0.0370 chunk 186 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 171 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 359 optimal weight: 30.0000 chunk 380 optimal weight: 9.9990 chunk 187 optimal weight: 0.8980 chunk 340 optimal weight: 0.0010 chunk 102 optimal weight: 2.9990 overall best weight: 0.7266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 87 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN L 38 GLN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 31981 Z= 0.172 Angle : 0.522 9.433 43532 Z= 0.272 Chirality : 0.043 0.299 4993 Planarity : 0.004 0.053 5590 Dihedral : 4.023 33.697 4270 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.06 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 3938 helix: 1.53 (0.21), residues: 638 sheet: -0.05 (0.18), residues: 828 loop : -1.05 (0.13), residues: 2472 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 3.422 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 162 average time/residue: 0.3889 time to fit residues: 110.7097 Evaluate side-chains 137 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 3.516 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2999 time to fit residues: 9.2787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 317 optimal weight: 3.9990 chunk 216 optimal weight: 0.0570 chunk 5 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 324 optimal weight: 1.9990 chunk 263 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 341 optimal weight: 20.0000 chunk 96 optimal weight: 0.6980 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 31981 Z= 0.244 Angle : 0.539 9.552 43532 Z= 0.280 Chirality : 0.043 0.304 4993 Planarity : 0.004 0.053 5590 Dihedral : 4.055 33.900 4270 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.85 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 3938 helix: 1.40 (0.21), residues: 640 sheet: -0.09 (0.18), residues: 831 loop : -1.05 (0.13), residues: 2467 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 15 residues processed: 178 average time/residue: 0.3855 time to fit residues: 121.8314 Evaluate side-chains 144 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 3.623 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2894 time to fit residues: 14.1434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 128 optimal weight: 6.9990 chunk 342 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 223 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 381 optimal weight: 9.9990 chunk 316 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN L 50 GLN W 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 31981 Z= 0.179 Angle : 0.521 9.597 43532 Z= 0.268 Chirality : 0.043 0.300 4993 Planarity : 0.004 0.052 5590 Dihedral : 3.974 34.793 4270 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 3938 helix: 1.47 (0.21), residues: 645 sheet: -0.07 (0.18), residues: 840 loop : -1.00 (0.13), residues: 2453 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 3.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 8 residues processed: 163 average time/residue: 0.4001 time to fit residues: 114.5840 Evaluate side-chains 138 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 3.469 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2916 time to fit residues: 9.4546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 367 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 217 optimal weight: 0.8980 chunk 278 optimal weight: 0.0010 chunk 215 optimal weight: 0.1980 chunk 320 optimal weight: 1.9990 chunk 212 optimal weight: 0.0870 chunk 379 optimal weight: 30.0000 chunk 237 optimal weight: 0.4980 chunk 231 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 606 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 31981 Z= 0.136 Angle : 0.507 10.396 43532 Z= 0.261 Chirality : 0.043 0.301 4993 Planarity : 0.004 0.056 5590 Dihedral : 3.842 34.099 4270 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.18 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3938 helix: 1.65 (0.21), residues: 645 sheet: 0.04 (0.18), residues: 846 loop : -0.95 (0.13), residues: 2447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 3.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 158 average time/residue: 0.4120 time to fit residues: 114.4113 Evaluate side-chains 135 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 3.779 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2889 time to fit residues: 9.8638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 234 optimal weight: 7.9990 chunk 151 optimal weight: 20.0000 chunk 226 optimal weight: 0.0170 chunk 114 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 241 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1142 GLN C 448 ASN C 777 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 31981 Z= 0.227 Angle : 0.525 10.279 43532 Z= 0.271 Chirality : 0.043 0.328 4993 Planarity : 0.004 0.053 5590 Dihedral : 3.904 34.180 4270 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.12 % Favored : 93.83 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3938 helix: 1.66 (0.21), residues: 640 sheet: -0.06 (0.17), residues: 870 loop : -1.00 (0.13), residues: 2428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 144 average time/residue: 0.4145 time to fit residues: 103.9136 Evaluate side-chains 134 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 3.515 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2987 time to fit residues: 9.3631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 345 optimal weight: 0.8980 chunk 363 optimal weight: 7.9990 chunk 331 optimal weight: 10.0000 chunk 353 optimal weight: 40.0000 chunk 212 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 277 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 319 optimal weight: 0.9990 chunk 334 optimal weight: 9.9990 chunk 352 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 31981 Z= 0.177 Angle : 0.515 11.425 43532 Z= 0.264 Chirality : 0.043 0.303 4993 Planarity : 0.004 0.061 5590 Dihedral : 3.877 34.994 4270 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.93 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3938 helix: 1.70 (0.21), residues: 640 sheet: -0.09 (0.17), residues: 907 loop : -0.95 (0.13), residues: 2391 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 3.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 138 average time/residue: 0.4198 time to fit residues: 100.7224 Evaluate side-chains 136 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 3.178 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2706 time to fit residues: 8.5726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 232 optimal weight: 5.9990 chunk 374 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 260 optimal weight: 0.9990 chunk 392 optimal weight: 40.0000 chunk 361 optimal weight: 30.0000 chunk 312 optimal weight: 0.0040 chunk 32 optimal weight: 4.9990 chunk 241 optimal weight: 0.3980 chunk 191 optimal weight: 4.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 31981 Z= 0.196 Angle : 0.522 10.034 43532 Z= 0.268 Chirality : 0.043 0.362 4993 Planarity : 0.004 0.054 5590 Dihedral : 3.892 35.204 4270 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.12 % Favored : 93.85 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3938 helix: 1.70 (0.21), residues: 640 sheet: -0.12 (0.17), residues: 911 loop : -0.95 (0.13), residues: 2387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 135 average time/residue: 0.4105 time to fit residues: 96.6328 Evaluate side-chains 131 residues out of total 3440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 3.350 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2904 time to fit residues: 6.2884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 248 optimal weight: 7.9990 chunk 332 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 288 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 321 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1074 ASN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.142176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.084906 restraints weight = 83116.676| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 4.23 r_work: 0.3196 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 31981 Z= 0.342 Angle : 0.590 9.276 43532 Z= 0.305 Chirality : 0.045 0.360 4993 Planarity : 0.004 0.063 5590 Dihedral : 4.169 35.303 4270 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.98 % Favored : 92.99 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 3938 helix: 1.26 (0.21), residues: 653 sheet: -0.20 (0.17), residues: 902 loop : -1.09 (0.13), residues: 2383 =============================================================================== Job complete usr+sys time: 5821.47 seconds wall clock time: 107 minutes 50.23 seconds (6470.23 seconds total)