Starting phenix.real_space_refine on Sun Feb 18 19:28:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdh_22822/02_2024/7kdh_22822.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdh_22822/02_2024/7kdh_22822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdh_22822/02_2024/7kdh_22822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdh_22822/02_2024/7kdh_22822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdh_22822/02_2024/7kdh_22822.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdh_22822/02_2024/7kdh_22822.pdb" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.050 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 98 5.16 5 C 14449 2.51 5 N 3731 2.21 5 O 4420 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 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1118": "OD1" <-> "OD2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C ASP 1127": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22698 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 7486 Classifications: {'peptide': 970} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 45, 'TRANS': 924} Chain breaks: 11 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 7033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7033 Classifications: {'peptide': 958} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 44, 'TRANS': 913} Chain breaks: 11 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 608 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 12, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 8, 'GLU:plan': 4, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 316 Chain: "C" Number of atoms: 7367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7367 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 45, 'TRANS': 917} Chain breaks: 11 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ASN:plan1': 4, 'TYR:plan': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 103 Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Chain: "B" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 266 Unusual residues: {'NAG': 19} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 19 Chain: "C" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 294 Unusual residues: {'NAG': 21} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 21 Time building chain proxies: 12.31, per 1000 atoms: 0.54 Number of scatterers: 22698 At special positions: 0 Unit cell: (137.385, 126.735, 177.855, 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 98 16.00 O 4420 8.00 N 3731 7.00 C 14449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 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=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.99 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A 717 " " NAG A1312 " - " ASN A 801 " " NAG A1314 " - " ASN A1074 " " NAG A1315 " - " ASN A1098 " " NAG A1317 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 343 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 61 " " NAG B1313 " - " ASN B 165 " " NAG B1314 " - " ASN B 801 " " NAG B1315 " - " ASN B 657 " " NAG B1317 " - " ASN B 709 " " NAG B1318 " - " ASN B1098 " " NAG B1319 " - " ASN B 282 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 234 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C 122 " " NAG C1309 " - " ASN C 717 " " NAG C1310 " - " ASN C 282 " " NAG C1311 " - " ASN C 343 " " NAG C1312 " - " ASN C 603 " " NAG C1315 " - " ASN C 657 " " NAG C1317 " - " ASN C1134 " " NAG C1319 " - " ASN C 801 " " NAG C1320 " - " ASN C 616 " " NAG C1321 " - " ASN C1098 " Time building additional restraints: 8.83 Conformation dependent library (CDL) restraints added in 4.3 seconds 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5432 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 42 sheets defined 28.0% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.635A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.679A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.804A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.253A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.946A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.998A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) 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 removed outlier: 3.856A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.722A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.756A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.479A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.432A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.688A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.959A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 3.674A pdb=" N ALA B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.704A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.727A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 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 984 removed outlier: 3.820A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.290A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.303A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.011A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.345A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.618A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.660A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.620A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.679A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.726A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.679A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.613A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.865A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.807A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.587A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.624A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.516A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.321A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.579A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.814A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.769A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.161A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.823A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.786A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.336A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.275A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 10.066A pdb=" N SER B 221 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ARG B 34 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N LEU B 223 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.719A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.261A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.329A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 357 removed outlier: 5.415A pdb=" N PHE B 515 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR B 396 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU B 513 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 398 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 511 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE B 400 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG B 509 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 402 " --> pdb=" O PRO B 507 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 357 Processing sheet with id=AC6, first strand: chain 'B' and resid 448 through 453 removed outlier: 3.657A pdb=" N ASN B 450 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR B 495 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU B 452 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLN B 493 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.148A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.751A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.543A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.543A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 3.906A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.006A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.827A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.615A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.720A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.738A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.148A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.832A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.656A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.510A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1097 1009 hydrogen bonds defined for protein. 2757 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: 10.43 Time building geometry restraints manager: 9.44 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: 5458 1.33 - 1.45: 4645 1.45 - 1.58: 12930 1.58 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 23155 Sorted by residual: bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C1 NAG A1313 " pdb=" O5 NAG A1313 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1 NAG A1316 " pdb=" O5 NAG A1316 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 23150 not shown) Histogram of bond angle deviations from ideal: 96.29 - 104.62: 329 104.62 - 112.94: 11908 112.94 - 121.27: 12964 121.27 - 129.59: 6294 129.59 - 137.91: 41 Bond angle restraints: 31536 Sorted by residual: angle pdb=" CA VAL B 510 " pdb=" CB VAL B 510 " pdb=" CG1 VAL B 510 " ideal model delta sigma weight residual 110.40 130.86 -20.46 1.70e+00 3.46e-01 1.45e+02 angle pdb=" CA VAL B 433 " pdb=" CB VAL B 433 " pdb=" CG1 VAL B 433 " ideal model delta sigma weight residual 110.40 130.35 -19.95 1.70e+00 3.46e-01 1.38e+02 angle pdb=" CA VAL B 512 " pdb=" CB VAL B 512 " pdb=" CG1 VAL B 512 " ideal model delta sigma weight residual 110.40 127.16 -16.76 1.70e+00 3.46e-01 9.72e+01 angle pdb=" CB LEU B 141 " pdb=" CG LEU B 141 " pdb=" CD1 LEU B 141 " ideal model delta sigma weight residual 110.70 137.91 -27.21 3.00e+00 1.11e-01 8.23e+01 angle pdb=" CA ASN A 331 " pdb=" CB ASN A 331 " pdb=" CG ASN A 331 " ideal model delta sigma weight residual 112.60 119.49 -6.89 1.00e+00 1.00e+00 4.74e+01 ... (remaining 31531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.58: 13562 18.58 - 37.16: 759 37.16 - 55.73: 131 55.73 - 74.31: 41 74.31 - 92.89: 22 Dihedral angle restraints: 14515 sinusoidal: 6120 harmonic: 8395 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -174.62 88.62 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 179.87 -86.87 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 177.15 -84.15 1 1.00e+01 1.00e-02 8.62e+01 ... (remaining 14512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.697: 3814 0.697 - 1.394: 1 1.394 - 2.090: 20 2.090 - 2.787: 2 2.787 - 3.484: 3 Chirality restraints: 3840 Sorted by residual: chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -5.88 3.48 2.00e-01 2.50e+01 3.03e+02 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -5.74 3.34 2.00e-01 2.50e+01 2.79e+02 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -5.25 2.85 2.00e-01 2.50e+01 2.03e+02 ... (remaining 3837 not shown) Planarity restraints: 4032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " 0.162 2.00e-02 2.50e+03 1.70e-01 3.60e+02 pdb=" CG ASN C 657 " -0.101 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " -0.258 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " -0.005 2.00e-02 2.50e+03 pdb=" C1 NAG C1315 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 282 " -0.160 2.00e-02 2.50e+03 1.67e-01 3.50e+02 pdb=" CG ASN B 282 " 0.093 2.00e-02 2.50e+03 pdb=" OD1 ASN B 282 " 0.257 2.00e-02 2.50e+03 pdb=" ND2 ASN B 282 " 0.009 2.00e-02 2.50e+03 pdb=" C1 NAG B1319 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.143 2.00e-02 2.50e+03 1.52e-01 2.88e+02 pdb=" CG ASN C1074 " -0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.233 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " 0.182 2.00e-02 2.50e+03 ... (remaining 4029 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 22 2.14 - 2.83: 5788 2.83 - 3.52: 30638 3.52 - 4.21: 52473 4.21 - 4.90: 91177 Nonbonded interactions: 180098 Sorted by model distance: nonbonded pdb=" OD1 ASN A1134 " pdb=" C1 NAG A1317 " model vdw 1.454 2.776 nonbonded pdb=" OD1 ASN B 657 " pdb=" C1 NAG B1315 " model vdw 1.462 2.776 nonbonded pdb=" OD1 ASN B 61 " pdb=" C1 NAG B1311 " model vdw 1.465 2.776 nonbonded pdb=" OD1 ASN C 282 " pdb=" C1 NAG C1310 " model vdw 1.469 2.776 nonbonded pdb=" OD1 ASN A 343 " pdb=" C1 NAG A1305 " model vdw 1.470 2.776 ... (remaining 180093 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 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 and (name N or name CA or name C or name O or name C \ B )) or resid 166 through 168 or (resid 169 and (name N or name CA or name C or \ name O or name CB )) or resid 170 through 171 or (resid 172 and (name N or name \ CA or name C or name O or name CB )) or resid 186 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 196 or \ (resid 197 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 8 through 213 or (resid 214 through 215 and (name N or name CA or name C or name \ O or name CB )) or resid 216 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (nam \ e N or name CA or name C or name O or name CB )) or resid 240 through 308 or (re \ sid 309 and (name N or name CA or name C or name O or name CB )) or resid 310 th \ rough 333 or (resid 334 and (name N or name CA or name C or name O or name CB )) \ or resid 335 through 345 or (resid 346 through 355 and (name N or name CA or na \ me C or name O or name CB )) or resid 356 or (resid 357 through 360 and (name N \ or name CA or name C or name O or name CB )) or resid 361 or (resid 362 through \ 376 and (name N or name CA or name C or name O or name CB )) or resid 377 or (re \ sid 378 and (name N or name CA or name C or name O or name CB )) or resid 379 or \ (resid 380 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 1 or (resid 382 through 383 and (name N or name CA or name C or name O or name C \ B )) or resid 384 or (resid 385 through 387 and (name N or name CA or name C or \ name O or name CB )) or resid 388 or (resid 389 through 390 and (name N or name \ CA or name C or name O or name CB )) or resid 391 or (resid 392 and (name N or n \ ame CA or name C or name O or name CB )) or resid 393 or (resid 394 through 403 \ and (name N or name CA or name C or name O or name CB )) or (resid 404 through 4 \ 11 and (name N or name CA or name C or name O or name CB )) or resid 412 through \ 413 or (resid 414 through 415 and (name N or name CA or name C or name O or nam \ e CB )) or resid 416 or (resid 417 through 425 and (name N or name CA or name C \ or name O or name CB )) or resid 426 or (resid 427 through 430 and (name N or na \ me CA or name C or name O or name CB )) or resid 431 through 433 or (resid 434 t \ hrough 435 and (name N or name CA or name C or name O or name CB )) or resid 436 \ or (resid 437 through 454 and (name N or name CA or name C or name O or name CB \ )) or (resid 462 and (name N or name CA or name C or name O or name CB )) or re \ sid 463 or (resid 464 through 466 and (name N or name CA or name C or name O or \ name CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or name \ C or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or \ name CA or name C or name O or name CB )) or resid 499 or (resid 500 through 50 \ 3 and (name N or name CA or name C or name O or name CB )) or (resid 504 through \ 506 and (name N or name CA or name C or name O or name CB )) or resid 507 throu \ gh 508 or (resid 509 and (name N or name CA or name C or name O or name CB )) or \ resid 510 or (resid 511 and (name N or name CA or name C or name O or name CB ) \ ) or resid 512 or (resid 513 through 515 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 522 through 524 and (name N or name CA or name C or \ name O or name CB )) or resid 525 through 527 or (resid 528 and (name N or name \ CA or name C or name O or name CB )) or resid 529 through 810 or (resid 811 and \ (name N or name CA or name C or name O or name CB )) or resid 813 through 827 or \ resid 855 through 866 or (resid 867 through 868 and (name N or name CA or name \ C or name O or name CB )) or resid 869 through 1141 or (resid 1142 and (name N o \ r name CA or name C or name O or name CB )) or resid 1143 through 1144 or (resid \ 1145 through 1146 and (name N or name CA or name C or name O or name CB )) or r \ esid 1147 or resid 1301 through 1318)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or resid 16 \ 6 through 168 or (resid 169 and (name N or name CA or name C or name O or name C \ B )) or resid 170 through 190 or (resid 191 and (name N or name CA or name C or \ name O or name CB )) or resid 192 through 195 or (resid 196 through 197 and (nam \ e N or name CA or name C or name O or name CB )) or resid 198 through 241 or (re \ sid 242 through 264 and (name N or name CA or name C or name O or name CB )) or \ resid 265 through 280 or (resid 281 and (name N or name CA or name C or name O o \ r name CB )) or resid 282 through 339 or (resid 340 and (name N or name CA or na \ me C or name O or name CB )) or resid 341 through 442 or resid 448 through 464 o \ r (resid 465 through 466 and (name N or name CA or name C or name O or name CB ) \ ) or resid 491 through 501 or resid 503 through 567 or (resid 568 and (name N or \ name CA or name C or name O or name CB )) or resid 569 through 582 or (resid 58 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 584 through \ 585 or (resid 586 and (name N or name CA or name C or name O or name CB )) or re \ sid 587 through 613 or (resid 614 and (name N or name CA or name C or name O or \ name CB )) or resid 615 through 618 or (resid 619 and (name N or name CA or name \ C or name O or name CB )) or resid 620 through 676 or resid 690 through 744 or \ (resid 745 and (name N or name CA or name C or name O or name CB )) or resid 746 \ through 747 or (resid 748 and (name N or name CA or name C or name O or name CB \ )) or resid 749 through 810 or (resid 811 and (name N or name CA or name C or n \ ame O or name CB )) or resid 813 or (resid 814 and (name N or name CA or name C \ or name O or name CB )) or resid 815 through 827 or resid 855 through 866 or (re \ sid 867 through 868 and (name N or name CA or name C or name O or name CB )) or \ resid 869 through 1091 or (resid 1092 and (name N or name CA or name C or name O \ or name CB )) or resid 1093 through 1143 or (resid 1144 through 1146 and (name \ N or name CA or name C or name O or name CB )) or resid 1147 or resid 1301 throu \ gh 1318)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 through 195 or (resid 196 th \ rough 197 and (name N or name CA or name C or name O or name CB )) or resid 198 \ through 213 or (resid 214 through 215 and (name N or name CA or name C or name O \ or name CB )) or resid 216 through 217 or (resid 218 and (name N or name CA or \ name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (name \ N or name CA or name C or name O or name CB )) or resid 240 through 308 or (resi \ d 309 and (name N or name CA or name C or name O or name CB )) or resid 310 thro \ ugh 333 or (resid 334 and (name N or name CA or name C or name O or name CB )) o \ r resid 335 through 339 or (resid 340 and (name N or name CA or name C or name O \ or name CB )) or resid 341 through 345 or (resid 346 through 355 and (name N or \ name CA or name C or name O or name CB )) or resid 356 or (resid 357 through 36 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 361 or (resi \ d 362 through 376 and (name N or name CA or name C or name O or name CB )) or re \ sid 377 through 379 or (resid 380 and (name N or name CA or name C or name O or \ name CB )) or resid 381 or (resid 382 through 383 and (name N or name CA or name \ C or name O or name CB )) or resid 384 or (resid 385 through 387 and (name N or \ name CA or name C or name O or name CB )) or resid 388 or (resid 389 through 39 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 391 or (resi \ d 392 and (name N or name CA or name C or name O or name CB )) or resid 393 or ( \ resid 394 through 403 and (name N or name CA or name C or name O or name CB )) o \ r (resid 404 through 411 and (name N or name CA or name C or name O or name CB ) \ ) or resid 412 through 413 or (resid 414 through 415 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 416 through 425 and (name N or name CA o \ r name C or name O or name CB )) or resid 426 or (resid 427 through 430 and (nam \ e N or name CA or name C or name O or name CB )) or resid 431 through 433 or (re \ sid 434 through 435 and (name N or name CA or name C or name O or name CB )) or \ resid 436 through 437 or (resid 438 through 442 and (name N or name CA or name C \ or name O or name CB )) or (resid 448 through 462 and (name N or name CA or nam \ e C or name O or name CB )) or resid 463 or (resid 464 through 466 and (name N o \ r name CA or name C or name O or name CB )) or resid 491 or (resid 492 through 4 \ 95 and (name N or name CA or name C or name O or name CB )) or resid 496 or (res \ id 497 through 498 and (name N or name CA or name C or name O or name CB )) or r \ esid 499 through 500 or (resid 501 and (name N or name CA or name C or name O or \ name CB )) or (resid 503 and (name N or name CA or name C or name O or name CB \ )) or (resid 504 through 506 and (name N or name CA or name C or name O or name \ CB )) or resid 507 through 508 or (resid 509 and (name N or name CA or name C or \ name O or name CB )) or resid 510 or (resid 511 and (name N or name CA or name \ C or name O or name CB )) or resid 512 or (resid 513 through 515 and (name N or \ name CA or name C or name O or name CB )) or (resid 522 through 524 and (name N \ or name CA or name C or name O or name CB )) or resid 525 through 527 or (resid \ 528 and (name N or name CA or name C or name O or name CB )) or resid 529 throug \ h 567 or (resid 568 and (name N or name CA or name C or name O or name CB )) or \ resid 569 through 582 or (resid 583 and (name N or name CA or name C or name O o \ r name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or na \ me C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 813 or (resid \ 814 and (name N or name CA or name C or name O or name CB )) or resid 815 throug \ h 1091 or (resid 1092 and (name N or name CA or name C or name O or name CB )) o \ r resid 1093 through 1141 or (resid 1142 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name \ CA or name C or name O or name CB )) or resid 1147 or resid 1301 through 1318)) } 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: 1.950 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: 0.010 Extract box with map and model: 7.080 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 62.730 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.100 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 : 0.013 0.082 23155 Z= 0.880 Angle : 1.770 27.215 31536 Z= 1.168 Chirality : 0.191 3.484 3840 Planarity : 0.014 0.155 3987 Dihedral : 12.764 92.889 8978 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 0.56 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.31 % Favored : 92.30 % Rotamer: Outliers : 0.56 % Allowed : 2.83 % Favored : 96.62 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 2819 helix: -0.57 (0.17), residues: 665 sheet: -0.02 (0.23), residues: 477 loop : -1.23 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.203 0.030 TRP C 886 HIS 0.017 0.003 HIS A1048 PHE 0.095 0.013 PHE B 927 TYR 0.203 0.022 TYR C 904 ARG 0.011 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 196 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1081 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7320 (pt) REVERT: B 1135 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.7201 (t0) outliers start: 13 outliers final: 3 residues processed: 206 average time/residue: 0.3306 time to fit residues: 109.6171 Evaluate side-chains 97 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 8.9990 chunk 218 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 168 optimal weight: 0.6980 chunk 261 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS A1119 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23155 Z= 0.192 Angle : 0.680 8.169 31536 Z= 0.357 Chirality : 0.048 0.345 3840 Planarity : 0.004 0.031 3987 Dihedral : 7.056 54.597 4276 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.04 % Favored : 95.89 % Rotamer: Outliers : 1.16 % Allowed : 5.74 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.38 (0.15), residues: 2819 helix: 1.46 (0.20), residues: 651 sheet: -0.21 (0.19), residues: 660 loop : -1.05 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 436 HIS 0.004 0.001 HIS A 49 PHE 0.020 0.002 PHE A 168 TYR 0.019 0.002 TYR B 170 ARG 0.006 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 134 average time/residue: 0.3260 time to fit residues: 72.5198 Evaluate side-chains 93 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 217 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 262 optimal weight: 7.9990 chunk 283 optimal weight: 0.9980 chunk 233 optimal weight: 0.7980 chunk 259 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23155 Z= 0.252 Angle : 0.593 7.371 31536 Z= 0.310 Chirality : 0.046 0.224 3840 Planarity : 0.004 0.058 3987 Dihedral : 6.136 56.247 4270 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.93 % Favored : 95.03 % Rotamer: Outliers : 1.54 % Allowed : 7.07 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.14 (0.15), residues: 2819 helix: 1.71 (0.20), residues: 667 sheet: -0.21 (0.19), residues: 699 loop : -0.88 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 104 HIS 0.004 0.001 HIS B1048 PHE 0.026 0.002 PHE B 201 TYR 0.021 0.002 TYR A1067 ARG 0.003 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 90 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 21 residues processed: 118 average time/residue: 0.2913 time to fit residues: 58.9613 Evaluate side-chains 99 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 1.9990 chunk 196 optimal weight: 20.0000 chunk 135 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 125 optimal weight: 40.0000 chunk 175 optimal weight: 7.9990 chunk 262 optimal weight: 0.9980 chunk 278 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 249 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 804 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23155 Z= 0.220 Angle : 0.552 8.639 31536 Z= 0.286 Chirality : 0.044 0.201 3840 Planarity : 0.003 0.051 3987 Dihedral : 5.717 62.970 4270 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.07 % Allowed : 8.35 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.03 (0.16), residues: 2819 helix: 1.92 (0.21), residues: 661 sheet: -0.20 (0.19), residues: 700 loop : -0.83 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.003 0.001 HIS B1048 PHE 0.027 0.001 PHE B 201 TYR 0.018 0.001 TYR A1067 ARG 0.002 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 LEU cc_start: 0.7647 (mp) cc_final: 0.7443 (mt) outliers start: 25 outliers final: 16 residues processed: 103 average time/residue: 0.3000 time to fit residues: 53.6802 Evaluate side-chains 90 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 207 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 249 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN B 901 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23155 Z= 0.266 Angle : 0.550 7.069 31536 Z= 0.285 Chirality : 0.044 0.213 3840 Planarity : 0.003 0.044 3987 Dihedral : 5.551 68.081 4270 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.37 % Allowed : 8.74 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.03 (0.16), residues: 2819 helix: 1.88 (0.20), residues: 669 sheet: -0.24 (0.19), residues: 696 loop : -0.79 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 104 HIS 0.003 0.001 HIS B1048 PHE 0.021 0.001 PHE B1121 TYR 0.020 0.001 TYR B1067 ARG 0.002 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 84 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 21 residues processed: 108 average time/residue: 0.3174 time to fit residues: 59.6223 Evaluate side-chains 93 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 4.9990 chunk 250 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 68 optimal weight: 0.0070 chunk 278 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 129 optimal weight: 50.0000 chunk 23 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 23155 Z= 0.154 Angle : 0.515 10.526 31536 Z= 0.266 Chirality : 0.043 0.224 3840 Planarity : 0.003 0.042 3987 Dihedral : 5.227 72.886 4270 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.99 % Allowed : 9.46 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2819 helix: 2.09 (0.21), residues: 666 sheet: -0.16 (0.19), residues: 698 loop : -0.68 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 104 HIS 0.002 0.000 HIS C 655 PHE 0.030 0.001 PHE B 201 TYR 0.018 0.001 TYR B1067 ARG 0.003 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 18 residues processed: 101 average time/residue: 0.2999 time to fit residues: 53.3586 Evaluate side-chains 91 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 277 optimal weight: 0.0370 chunk 173 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 128 optimal weight: 0.0470 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 23155 Z= 0.201 Angle : 0.519 12.125 31536 Z= 0.265 Chirality : 0.043 0.209 3840 Planarity : 0.003 0.040 3987 Dihedral : 5.112 73.938 4270 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.11 % Allowed : 9.76 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2819 helix: 2.09 (0.21), residues: 665 sheet: -0.13 (0.19), residues: 707 loop : -0.65 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 104 HIS 0.003 0.001 HIS C1048 PHE 0.024 0.001 PHE B 201 TYR 0.018 0.001 TYR B1067 ARG 0.002 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 238 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.5164 (p90) REVERT: C 1005 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7300 (tm-30) outliers start: 26 outliers final: 19 residues processed: 98 average time/residue: 0.3059 time to fit residues: 53.2532 Evaluate side-chains 94 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 73 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 218 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23155 Z= 0.191 Angle : 0.512 10.382 31536 Z= 0.261 Chirality : 0.043 0.207 3840 Planarity : 0.003 0.039 3987 Dihedral : 4.997 68.192 4270 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.16 % Allowed : 9.72 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2819 helix: 2.10 (0.21), residues: 666 sheet: -0.12 (0.19), residues: 705 loop : -0.59 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 104 HIS 0.004 0.001 HIS C1064 PHE 0.023 0.001 PHE B 201 TYR 0.018 0.001 TYR B1067 ARG 0.001 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 72 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 238 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.5189 (p90) REVERT: B 900 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7788 (mtp) outliers start: 27 outliers final: 22 residues processed: 95 average time/residue: 0.3020 time to fit residues: 51.6960 Evaluate side-chains 94 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 5.9990 chunk 265 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 chunk 258 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 203 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 257 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23155 Z= 0.188 Angle : 0.502 8.864 31536 Z= 0.256 Chirality : 0.043 0.209 3840 Planarity : 0.003 0.040 3987 Dihedral : 4.826 56.657 4270 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.16 % Allowed : 9.89 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2819 helix: 2.14 (0.21), residues: 668 sheet: -0.13 (0.19), residues: 697 loop : -0.56 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 104 HIS 0.004 0.001 HIS B1048 PHE 0.029 0.001 PHE B 201 TYR 0.016 0.001 TYR B1067 ARG 0.002 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 74 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 238 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.5140 (p90) REVERT: C 1005 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7283 (tm-30) outliers start: 27 outliers final: 21 residues processed: 98 average time/residue: 0.2820 time to fit residues: 49.1335 Evaluate side-chains 92 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 69 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 2.9990 chunk 273 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 264 optimal weight: 0.9990 chunk 228 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 23155 Z= 0.229 Angle : 0.526 9.891 31536 Z= 0.268 Chirality : 0.043 0.212 3840 Planarity : 0.003 0.039 3987 Dihedral : 4.849 53.245 4270 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.99 % Allowed : 9.85 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.16), residues: 2819 helix: 2.10 (0.21), residues: 666 sheet: -0.16 (0.19), residues: 699 loop : -0.58 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 104 HIS 0.002 0.001 HIS B1064 PHE 0.028 0.001 PHE B 201 TYR 0.018 0.001 TYR B1067 ARG 0.002 0.000 ARG A 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 2.468 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: B 238 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.5217 (p90) outliers start: 23 outliers final: 21 residues processed: 90 average time/residue: 0.2812 time to fit residues: 45.1641 Evaluate side-chains 89 residues out of total 2536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 210 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 228 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.091871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.063265 restraints weight = 60200.134| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.30 r_work: 0.3014 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23155 Z= 0.173 Angle : 0.502 9.203 31536 Z= 0.255 Chirality : 0.043 0.210 3840 Planarity : 0.003 0.039 3987 Dihedral : 4.691 46.468 4270 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.99 % Allowed : 10.15 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2819 helix: 2.18 (0.21), residues: 667 sheet: -0.09 (0.19), residues: 687 loop : -0.55 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 104 HIS 0.002 0.000 HIS C1048 PHE 0.029 0.001 PHE B 201 TYR 0.017 0.001 TYR B1067 ARG 0.002 0.000 ARG C 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3783.76 seconds wall clock time: 70 minutes 37.51 seconds (4237.51 seconds total)