Starting phenix.real_space_refine (version: dev) on Thu Dec 22 10:50:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeb_31076/12_2022/7eeb_31076.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeb_31076/12_2022/7eeb_31076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeb_31076/12_2022/7eeb_31076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeb_31076/12_2022/7eeb_31076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeb_31076/12_2022/7eeb_31076.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeb_31076/12_2022/7eeb_31076.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.083 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 379": "NH1" <-> "NH2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 223": "NH1" <-> "NH2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 152": "NH1" <-> "NH2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D GLU 287": "OE1" <-> "OE2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 221": "OE1" <-> "OE2" Residue "E PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 307": "OE1" <-> "OE2" Residue "E GLU 380": "OE1" <-> "OE2" Residue "E ASP 390": "OD1" <-> "OD2" Residue "E GLU 579": "OE1" <-> "OE2" Residue "E GLU 608": "OE1" <-> "OE2" Residue "E GLU 616": "OE1" <-> "OE2" Residue "E TYR 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 813": "OE1" <-> "OE2" Residue "E TYR 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 898": "NH1" <-> "NH2" Residue "E TYR 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 958": "OE1" <-> "OE2" Residue "E GLU 962": "OE1" <-> "OE2" Residue "E GLU 1043": "OE1" <-> "OE2" Residue "E ASP 1050": "OD1" <-> "OD2" Residue "E GLU 1051": "OE1" <-> "OE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "F GLU 112": "OE1" <-> "OE2" Residue "F ASP 258": "OD1" <-> "OD2" Residue "F PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 359": "OE1" <-> "OE2" Residue "F GLU 370": "OE1" <-> "OE2" Residue "F GLU 455": "OE1" <-> "OE2" Residue "F TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 501": "OE1" <-> "OE2" Residue "F TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 654": "OE1" <-> "OE2" Residue "F GLU 665": "OE1" <-> "OE2" Residue "F GLU 729": "OE1" <-> "OE2" Residue "F PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 909": "OD1" <-> "OD2" Residue "F PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 951": "NH1" <-> "NH2" Residue "F GLU 961": "OE1" <-> "OE2" Residue "F TYR 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1024": "OE1" <-> "OE2" Residue "F ARG 1061": "NH1" <-> "NH2" Residue "F PHE 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G GLU 223": "OE1" <-> "OE2" Residue "G TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G GLU 287": "OE1" <-> "OE2" Residue "G GLU 309": "OE1" <-> "OE2" Residue "G GLU 390": "OE1" <-> "OE2" Residue "G GLU 418": "OE1" <-> "OE2" Residue "G GLU 440": "OE1" <-> "OE2" Residue "G PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 563": "OE1" <-> "OE2" Residue "G TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 593": "OE1" <-> "OE2" Residue "G PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 666": "OE1" <-> "OE2" Residue "H GLU 287": "OE1" <-> "OE2" Residue "H GLU 477": "OE1" <-> "OE2" Residue "H GLU 591": "OE1" <-> "OE2" Residue "H GLU 649": "OE1" <-> "OE2" Residue "H GLU 719": "OE1" <-> "OE2" Residue "H ARG 756": "NH1" <-> "NH2" Residue "H GLU 801": "OE1" <-> "OE2" Residue "H GLU 841": "OE1" <-> "OE2" Residue "H GLU 850": "OE1" <-> "OE2" Residue "H TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 928": "OE1" <-> "OE2" Residue "L GLU 465": "OE1" <-> "OE2" Residue "L PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 508": "NH1" <-> "NH2" Residue "L GLU 549": "OE1" <-> "OE2" Residue "L ASP 561": "OD1" <-> "OD2" Residue "L ASP 563": "OD1" <-> "OD2" Residue "M ARG 52": "NH1" <-> "NH2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M ARG 112": "NH1" <-> "NH2" Residue "M ARG 115": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 47874 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2112 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 4, 'TRANS': 253} Chain: "B" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2343 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 4, 'TRANS': 276} Chain: "C" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2277 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 2, 'TRANS': 275} Chain: "D" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1965 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain: "E" Number of atoms: 8470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8470 Classifications: {'peptide': 1053} Link IDs: {'PTRANS': 58, 'TRANS': 994} Chain breaks: 2 Chain: "F" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8454 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 50, 'TRANS': 991} Chain: "G" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5680 Classifications: {'peptide': 714} Link IDs: {'PTRANS': 30, 'TRANS': 683} Chain breaks: 2 Chain: "H" Number of atoms: 7502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 7502 Classifications: {'peptide': 916} Link IDs: {'PTRANS': 40, 'TRANS': 875} Chain breaks: 1 Chain: "L" Number of atoms: 4694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4694 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 23, 'TRANS': 573} Chain breaks: 1 Chain: "J" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 794 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PTRANS': 6, 'TRANS': 154} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 564 Unresolved non-hydrogen angles: 728 Unresolved non-hydrogen dihedrals: 489 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 2, 'TYR:plan': 10, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 9, 'GLU:plan': 5, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 320 Chain: "M" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 946 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "N" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 Chain: "I" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 863 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 162} Link IDs: {'PTRANS': 2, 'TRANS': 171} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 656 Unresolved non-hydrogen angles: 848 Unresolved non-hydrogen dihedrals: 561 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 10, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 17, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 394 Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 710 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 490 Unresolved non-hydrogen angles: 621 Unresolved non-hydrogen dihedrals: 404 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 298 Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {' NA': 1, '9Z9': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 26.76, per 1000 atoms: 0.56 Number of scatterers: 47874 At special positions: 0 Unit cell: (178.832, 182.064, 238.083, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 262 16.00 Na 2 11.00 O 8797 8.00 N 7669 7.00 C 31144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 302 " distance=2.03 Simple disulfide: pdb=" SG CYS E 330 " - pdb=" SG CYS E 343 " distance=2.03 Simple disulfide: pdb=" SG CYS E 720 " - pdb=" SG CYS E 818 " distance=1.50 Simple disulfide: pdb=" SG CYS E 831 " - pdb=" SG CYS E1039 " distance=1.93 Simple disulfide: pdb=" SG CYS E 913 " - pdb=" SG CYS E 922 " distance=2.66 Simple disulfide: pdb=" SG CYS E 924 " - pdb=" SG CYS E 939 " distance=2.03 Simple disulfide: pdb=" SG CYS F 45 " - pdb=" SG CYS F 106 " distance=2.03 Simple disulfide: pdb=" SG CYS F 160 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 289 " - pdb=" SG CYS F 344 " distance=2.03 Simple disulfide: pdb=" SG CYS F 395 " - pdb=" SG CYS F 403 " distance=2.03 Simple disulfide: pdb=" SG CYS F 634 " - pdb=" SG CYS F 856 " distance=2.03 Simple disulfide: pdb=" SG CYS F 802 " - pdb=" SG CYS F 830 " distance=2.04 Simple disulfide: pdb=" SG CYS F 878 " - pdb=" SG CYS F1042 " distance=2.03 Simple disulfide: pdb=" SG CYS F 905 " - pdb=" SG CYS F 914 " distance=1.81 Simple disulfide: pdb=" SG CYS F1006 " - pdb=" SG CYS F1012 " distance=2.03 Simple disulfide: pdb=" SG CYS G 20 " - pdb=" SG CYS G 366 " distance=2.02 Simple disulfide: pdb=" SG CYS G 56 " - pdb=" SG CYS G 143 " distance=2.02 Simple disulfide: pdb=" SG CYS G 142 " - pdb=" SG CYS G 149 " distance=2.04 Simple disulfide: pdb=" SG CYS G 384 " - pdb=" SG CYS G 493 " distance=2.03 Simple disulfide: pdb=" SG CYS G 507 " - pdb=" SG CYS G 701 " distance=2.03 Simple disulfide: pdb=" SG CYS G 522 " - pdb=" SG CYS G 569 " distance=2.04 Simple disulfide: pdb=" SG CYS G 621 " - pdb=" SG CYS G 651 " distance=2.03 Simple disulfide: pdb=" SG CYS H 87 " - pdb=" SG CYS H 101 " distance=2.66 Simple disulfide: pdb=" SG CYS H 130 " - pdb=" SG CYS H 235 " distance=2.03 Simple disulfide: pdb=" SG CYS H 275 " - pdb=" SG CYS H 365 " distance=2.03 Simple disulfide: pdb=" SG CYS H 439 " - pdb=" SG CYS H 442 " distance=2.03 Simple disulfide: pdb=" SG CYS H 617 " - pdb=" SG CYS H 724 " distance=2.03 Simple disulfide: pdb=" SG CYS H 737 " - pdb=" SG CYS H 919 " distance=2.02 Simple disulfide: pdb=" SG CYS H 753 " - pdb=" SG CYS H 786 " distance=2.52 Simple disulfide: pdb=" SG CYS H 838 " - pdb=" SG CYS H 869 " distance=2.04 Simple disulfide: pdb=" SG CYS L 491 " - pdb=" SG CYS L 538 " distance=2.03 Simple disulfide: pdb=" SG CYS L 497 " - pdb=" SG CYS L 517 " distance=2.02 Simple disulfide: pdb=" SG CYS L 506 " - pdb=" SG CYS L 560 " distance=2.03 Simple disulfide: pdb=" SG CYS L 521 " - pdb=" SG CYS L 536 " 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 Atom "HETATM47341 O5 NAG Y 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM47830 O5 NAG G 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM47788 O5 NAG E1203 .*. O " rejected from bonding due to valence issues. Atom "HETATM47485 O5 NAG a 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-2 " BMA O 4 " - " BMA O 5 " BETA1-3 " BMA O 3 " - " BMA O 4 " " BMA O 6 " - " BMA O 7 " " BMA Y 3 " - " BMA Y 4 " " BMA Z 3 " - " BMA Z 7 " " BMA Z 4 " - " BMA Z 5 " " BMA c 3 " - " BMA c 4 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " BETA1-6 " BMA O 3 " - " BMA O 6 " " BMA Y 3 " - " BMA Y 5 " " BMA Z 3 " - " BMA Z 4 " " BMA Z 4 " - " BMA Z 6 " " BMA c 3 " - " BMA c 5 " NAG-ASN " NAG E1201 " - " ASN E 672 " " NAG E1202 " - " ASN E 118 " " NAG E1203 " - " ASN E 915 " " NAG E1204 " - " ASN E 923 " " NAG F1201 " - " ASN F 402 " " NAG G 901 " - " ASN G 227 " " NAG G 902 " - " ASN G 535 " " NAG G 903 " - " ASN G 469 " " NAG H1001 " - " ASN H 749 " " NAG O 1 " - " ASN E 90 " " NAG P 1 " - " ASN E1017 " " NAG Q 1 " - " ASN F 103 " " NAG R 1 " - " ASN F 178 " " NAG S 1 " - " ASN F 672 " " NAG T 1 " - " ASN F 356 " " NAG U 1 " - " ASN G 627 " " NAG V 1 " - " ASN H 91 " " NAG W 1 " - " ASN H 143 " " NAG X 1 " - " ASN H 292 " " NAG Y 1 " - " ASN H 502 " " NAG Z 1 " - " ASN H 565 " " NAG a 1 " - " ASN H 920 " " NAG b 1 " - " ASN H 830 " " NAG c 1 " - " ASN H 888 " " NAG d 1 " - " ASN L 535 " Time building additional restraints: 20.00 Conformation dependent library (CDL) restraints added in 7.0 seconds 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11376 Finding SS restraints... Secondary structure from input PDB file: 167 helices and 76 sheets defined 38.9% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 352 through 371 Processing helix chain 'A' and resid 380 through 413 removed outlier: 3.655A pdb=" N VAL A 386 " --> pdb=" O TRP A 382 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLU A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 435 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.632A pdb=" N ARG A 449 " --> pdb=" O HIS A 445 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 4.150A pdb=" N ARG A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 465 " --> pdb=" O ARG A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 511 Proline residue: A 487 - end of helix removed outlier: 3.730A pdb=" N ALA A 491 " --> pdb=" O PRO A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.931A pdb=" N PHE A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 533 Processing helix chain 'A' and resid 537 through 549 removed outlier: 3.766A pdb=" N ILE A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR A 542 " --> pdb=" O TRP A 538 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 568 removed outlier: 4.183A pdb=" N ILE A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 594 removed outlier: 3.672A pdb=" N GLU A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 removed outlier: 3.764A pdb=" N ALA B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 129 removed outlier: 3.507A pdb=" N MET B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 166 removed outlier: 3.867A pdb=" N LEU B 142 " --> pdb=" O TRP B 138 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 4.006A pdb=" N TRP B 171 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 196 Proline residue: B 189 - end of helix Processing helix chain 'B' and resid 201 through 210 removed outlier: 3.813A pdb=" N GLN B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N CYS B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'B' and resid 215 through 221 removed outlier: 3.681A pdb=" N PHE B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 215 through 221' Processing helix chain 'B' and resid 224 through 239 Processing helix chain 'B' and resid 239 through 261 removed outlier: 3.682A pdb=" N LEU B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 293 Processing helix chain 'B' and resid 296 through 306 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 328 through 374 removed outlier: 3.975A pdb=" N VAL B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN B 368 " --> pdb=" O MET B 364 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 369 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 370 " --> pdb=" O LYS B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 48 Processing helix chain 'C' and resid 49 through 70 Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 79 through 104 Processing helix chain 'C' and resid 107 through 111 Processing helix chain 'C' and resid 112 through 134 removed outlier: 3.526A pdb=" N ILE C 116 " --> pdb=" O ASP C 112 " (cutoff:3.500A) Proline residue: C 128 - end of helix Processing helix chain 'C' and resid 141 through 148 removed outlier: 4.025A pdb=" N ALA C 145 " --> pdb=" O TYR C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 159 removed outlier: 4.223A pdb=" N ILE C 153 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 155 " --> pdb=" O ARG C 152 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 157 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR C 159 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 172 Processing helix chain 'C' and resid 173 through 200 removed outlier: 3.845A pdb=" N VAL C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 225 removed outlier: 4.284A pdb=" N PHE C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 238 removed outlier: 3.866A pdb=" N LEU C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 256 Processing helix chain 'C' and resid 259 through 315 removed outlier: 3.977A pdb=" N GLY C 265 " --> pdb=" O ASN C 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 66 Processing helix chain 'D' and resid 67 through 89 Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.805A pdb=" N GLN D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D 96 " --> pdb=" O TYR D 92 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 122 removed outlier: 3.540A pdb=" N LEU D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 131 through 149 removed outlier: 3.862A pdb=" N GLY D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE D 147 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE D 148 " --> pdb=" O PHE D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 160 through 165 Processing helix chain 'D' and resid 165 through 171 removed outlier: 4.094A pdb=" N VAL D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 213 removed outlier: 3.574A pdb=" N ILE D 180 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Proline residue: D 188 - end of helix removed outlier: 3.994A pdb=" N VAL D 203 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 235 Processing helix chain 'D' and resid 238 through 248 removed outlier: 3.821A pdb=" N ILE D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE D 246 " --> pdb=" O ILE D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 271 removed outlier: 3.938A pdb=" N VAL D 257 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'E' and resid 115 through 119 Processing helix chain 'E' and resid 156 through 161 removed outlier: 3.812A pdb=" N GLN E 160 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TRP E 161 " --> pdb=" O PRO E 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 156 through 161' Processing helix chain 'E' and resid 172 through 177 Proline residue: E 177 - end of helix Processing helix chain 'E' and resid 227 through 235 removed outlier: 3.637A pdb=" N GLU E 234 " --> pdb=" O ILE E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 293 removed outlier: 3.551A pdb=" N ARG E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 568 removed outlier: 5.279A pdb=" N TRP E 565 " --> pdb=" O ASN E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 574 removed outlier: 3.591A pdb=" N HIS E 573 " --> pdb=" O LYS E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 625 removed outlier: 4.137A pdb=" N LEU E 624 " --> pdb=" O SER E 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 685 through 689 Processing helix chain 'E' and resid 696 through 700 Processing helix chain 'E' and resid 846 through 853 Processing helix chain 'E' and resid 902 through 907 Processing helix chain 'E' and resid 925 through 931 Processing helix chain 'E' and resid 936 through 940 Processing helix chain 'E' and resid 997 through 1007 Proline residue: E1004 - end of helix Processing helix chain 'E' and resid 1059 through 1086 removed outlier: 3.745A pdb=" N LEU E1073 " --> pdb=" O VAL E1069 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE E1078 " --> pdb=" O ILE E1074 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU E1082 " --> pdb=" O PHE E1078 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 82 Processing helix chain 'F' and resid 110 through 121 Processing helix chain 'F' and resid 229 through 235 removed outlier: 4.089A pdb=" N PHE F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 397 Processing helix chain 'F' and resid 412 through 414 No H-bonds generated for 'chain 'F' and resid 412 through 414' Processing helix chain 'F' and resid 550 through 563 Processing helix chain 'F' and resid 604 through 611 Processing helix chain 'F' and resid 646 through 652 Processing helix chain 'F' and resid 671 through 692 Processing helix chain 'F' and resid 703 through 709 removed outlier: 3.971A pdb=" N TRP F 707 " --> pdb=" O PRO F 703 " (cutoff:3.500A) Processing helix chain 'F' and resid 710 through 713 Processing helix chain 'F' and resid 714 through 724 Processing helix chain 'F' and resid 734 through 736 No H-bonds generated for 'chain 'F' and resid 734 through 736' Processing helix chain 'F' and resid 776 through 780 Processing helix chain 'F' and resid 786 through 791 removed outlier: 4.344A pdb=" N LYS F 790 " --> pdb=" O ASN F 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 799 through 803 removed outlier: 3.607A pdb=" N CYS F 802 " --> pdb=" O ASP F 799 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU F 803 " --> pdb=" O PRO F 800 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 799 through 803' Processing helix chain 'F' and resid 835 through 839 removed outlier: 4.044A pdb=" N ASN F 839 " --> pdb=" O ILE F 836 " (cutoff:3.500A) Processing helix chain 'F' and resid 887 through 899 Processing helix chain 'F' and resid 960 through 969 Processing helix chain 'F' and resid 987 through 991 removed outlier: 3.873A pdb=" N LYS F 991 " --> pdb=" O GLU F 988 " (cutoff:3.500A) Processing helix chain 'F' and resid 1058 through 1083 removed outlier: 3.635A pdb=" N VAL F1068 " --> pdb=" O PHE F1064 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE F1072 " --> pdb=" O VAL F1068 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 155 removed outlier: 3.784A pdb=" N LEU G 150 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN G 155 " --> pdb=" O GLU G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 removed outlier: 3.608A pdb=" N SER G 189 " --> pdb=" O ASP G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 290 Processing helix chain 'G' and resid 370 through 374 Processing helix chain 'G' and resid 460 through 464 removed outlier: 4.070A pdb=" N GLY G 464 " --> pdb=" O GLN G 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 460 through 464' Processing helix chain 'G' and resid 467 through 472 removed outlier: 3.982A pdb=" N ALA G 472 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 528 through 534 Processing helix chain 'G' and resid 563 through 568 Processing helix chain 'G' and resid 724 through 741 removed outlier: 3.869A pdb=" N TRP G 738 " --> pdb=" O LEU G 734 " (cutoff:3.500A) Processing helix chain 'G' and resid 741 through 748 Processing helix chain 'H' and resid 159 through 164 Processing helix chain 'H' and resid 171 through 184 Processing helix chain 'H' and resid 309 through 314 Processing helix chain 'H' and resid 366 through 373 Processing helix chain 'H' and resid 393 through 395 No H-bonds generated for 'chain 'H' and resid 393 through 395' Processing helix chain 'H' and resid 403 through 410 Processing helix chain 'H' and resid 517 through 522 removed outlier: 3.741A pdb=" N LEU H 521 " --> pdb=" O ASN H 517 " (cutoff:3.500A) Processing helix chain 'H' and resid 601 through 614 Processing helix chain 'H' and resid 699 through 707 Processing helix chain 'H' and resid 780 through 785 Processing helix chain 'H' and resid 832 through 837 Processing helix chain 'H' and resid 844 through 852 Processing helix chain 'H' and resid 856 through 861 removed outlier: 4.046A pdb=" N TRP H 861 " --> pdb=" O LEU H 857 " (cutoff:3.500A) Processing helix chain 'H' and resid 868 through 872 removed outlier: 3.852A pdb=" N SER H 871 " --> pdb=" O PRO H 868 " (cutoff:3.500A) Processing helix chain 'H' and resid 937 through 967 removed outlier: 3.571A pdb=" N LEU H 944 " --> pdb=" O LEU H 940 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 957 " --> pdb=" O ILE H 953 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 90 removed outlier: 3.760A pdb=" N GLN L 88 " --> pdb=" O LEU L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 125 removed outlier: 3.681A pdb=" N LEU L 99 " --> pdb=" O GLY L 95 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE L 106 " --> pdb=" O ALA L 102 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA L 112 " --> pdb=" O GLY L 108 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL L 113 " --> pdb=" O ALA L 109 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 148 removed outlier: 3.736A pdb=" N TRP L 132 " --> pdb=" O THR L 128 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR L 133 " --> pdb=" O ARG L 129 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU L 134 " --> pdb=" O THR L 130 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP L 139 " --> pdb=" O MET L 135 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR L 140 " --> pdb=" O ASP L 136 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE L 148 " --> pdb=" O PHE L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 157 removed outlier: 3.786A pdb=" N LYS L 156 " --> pdb=" O HIS L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 177 removed outlier: 3.587A pdb=" N MET L 175 " --> pdb=" O GLY L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 184 removed outlier: 3.528A pdb=" N PHE L 182 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 207 removed outlier: 3.512A pdb=" N ILE L 207 " --> pdb=" O ARG L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 248 Proline residue: L 235 - end of helix removed outlier: 4.607A pdb=" N ILE L 241 " --> pdb=" O TYR L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 280 removed outlier: 4.211A pdb=" N GLY L 254 " --> pdb=" O THR L 250 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N PHE L 255 " --> pdb=" O SER L 251 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE L 259 " --> pdb=" O PHE L 255 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY L 267 " --> pdb=" O ALA L 263 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN L 277 " --> pdb=" O VAL L 273 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN L 278 " --> pdb=" O GLY L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 289 through 324 removed outlier: 3.631A pdb=" N ALA L 293 " --> pdb=" O GLU L 289 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN L 297 " --> pdb=" O ALA L 293 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU L 298 " --> pdb=" O LYS L 294 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN L 300 " --> pdb=" O TYR L 296 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU L 308 " --> pdb=" O TRP L 304 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE L 309 " --> pdb=" O LYS L 305 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA L 312 " --> pdb=" O LEU L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 328 through 340 Processing helix chain 'L' and resid 357 through 371 removed outlier: 3.559A pdb=" N HIS L 367 " --> pdb=" O HIS L 363 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE L 368 " --> pdb=" O ASN L 364 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU L 369 " --> pdb=" O ILE L 365 " (cutoff:3.500A) Processing helix chain 'L' and resid 371 through 402 removed outlier: 3.660A pdb=" N LEU L 375 " --> pdb=" O ASN L 371 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR L 376 " --> pdb=" O PRO L 372 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE L 379 " --> pdb=" O LEU L 375 " (cutoff:3.500A) Proline residue: L 396 - end of helix Processing helix chain 'L' and resid 406 through 416 removed outlier: 3.596A pdb=" N THR L 414 " --> pdb=" O ALA L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 417 through 437 removed outlier: 4.340A pdb=" N GLY L 421 " --> pdb=" O PHE L 417 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE L 424 " --> pdb=" O PRO L 420 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL L 433 " --> pdb=" O GLY L 429 " (cutoff:3.500A) Processing helix chain 'L' and resid 439 through 466 removed outlier: 3.534A pdb=" N VAL L 449 " --> pdb=" O LYS L 445 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER L 454 " --> pdb=" O THR L 450 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS L 466 " --> pdb=" O PHE L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 489 through 495 removed outlier: 3.666A pdb=" N GLU L 493 " --> pdb=" O ALA L 489 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS L 495 " --> pdb=" O CYS L 491 " (cutoff:3.500A) Processing helix chain 'L' and resid 565 through 595 removed outlier: 4.189A pdb=" N LEU L 569 " --> pdb=" O LEU L 565 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER L 576 " --> pdb=" O ALA L 572 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE L 586 " --> pdb=" O ASN L 582 " (cutoff:3.500A) Proline residue: L 587 - end of helix removed outlier: 3.502A pdb=" N ILE L 592 " --> pdb=" O VAL L 588 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU L 593 " --> pdb=" O ILE L 589 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN L 594 " --> pdb=" O SER L 590 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER L 595 " --> pdb=" O ILE L 591 " (cutoff:3.500A) Processing helix chain 'L' and resid 597 through 600 Processing helix chain 'L' and resid 601 through 614 removed outlier: 3.830A pdb=" N LEU L 605 " --> pdb=" O THR L 601 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY L 606 " --> pdb=" O SER L 602 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR L 608 " --> pdb=" O SER L 604 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE L 611 " --> pdb=" O VAL L 607 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS L 613 " --> pdb=" O TYR L 609 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE L 614 " --> pdb=" O ALA L 610 " (cutoff:3.500A) Processing helix chain 'L' and resid 618 through 632 removed outlier: 4.758A pdb=" N LEU L 622 " --> pdb=" O VAL L 618 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA L 631 " --> pdb=" O SER L 627 " (cutoff:3.500A) Processing helix chain 'L' and resid 652 through 689 removed outlier: 3.657A pdb=" N ILE L 668 " --> pdb=" O SER L 664 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE L 669 " --> pdb=" O SER L 665 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL L 670 " --> pdb=" O GLN L 666 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN L 678 " --> pdb=" O ILE L 674 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 17 removed outlier: 3.640A pdb=" N ILE J 10 " --> pdb=" O CYS J 6 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU J 17 " --> pdb=" O ASN J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 41 removed outlier: 3.841A pdb=" N ILE J 33 " --> pdb=" O TYR J 29 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU J 35 " --> pdb=" O MET J 31 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU J 39 " --> pdb=" O LEU J 35 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER J 40 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER J 41 " --> pdb=" O LEU J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 124 removed outlier: 3.805A pdb=" N GLY J 117 " --> pdb=" O MET J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 133 removed outlier: 3.865A pdb=" N ALA J 133 " --> pdb=" O PHE J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 160 removed outlier: 3.554A pdb=" N VAL J 154 " --> pdb=" O SER J 150 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN J 155 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS J 157 " --> pdb=" O ILE J 153 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR J 158 " --> pdb=" O VAL J 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 10 removed outlier: 3.869A pdb=" N ILE M 7 " --> pdb=" O TRP M 3 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU M 10 " --> pdb=" O ARG M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 removed outlier: 4.044A pdb=" N MET M 17 " --> pdb=" O PRO M 13 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU M 18 " --> pdb=" O PRO M 14 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU M 25 " --> pdb=" O ALA M 21 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL M 32 " --> pdb=" O ILE M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 79 removed outlier: 3.941A pdb=" N ILE M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA M 68 " --> pdb=" O SER M 64 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR M 74 " --> pdb=" O MET M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 102 removed outlier: 3.814A pdb=" N LEU M 88 " --> pdb=" O ARG M 84 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR M 89 " --> pdb=" O CYS M 85 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE M 90 " --> pdb=" O PHE M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 108 Processing helix chain 'N' and resid 11 through 30 removed outlier: 3.645A pdb=" N UNK N 15 " --> pdb=" O UNK N 11 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N UNK N 16 " --> pdb=" O UNK N 12 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N UNK N 17 " --> pdb=" O UNK N 13 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N UNK N 24 " --> pdb=" O UNK N 20 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N UNK N 27 " --> pdb=" O UNK N 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 18 Processing helix chain 'I' and resid 24 through 37 Processing helix chain 'I' and resid 46 through 57 Processing helix chain 'I' and resid 60 through 72 Processing helix chain 'I' and resid 81 through 92 Processing helix chain 'I' and resid 96 through 106 removed outlier: 3.829A pdb=" N ASP I 100 " --> pdb=" O ASP I 96 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS I 101 " --> pdb=" O HIS I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 137 through 149 Processing helix chain 'I' and resid 157 through 174 Processing helix chain 'K' and resid 42 through 47 Processing helix chain 'K' and resid 56 through 75 Processing helix chain 'K' and resid 77 through 94 Processing helix chain 'K' and resid 101 through 112 Processing helix chain 'K' and resid 112 through 135 removed outlier: 3.690A pdb=" N GLU K 116 " --> pdb=" O SER K 112 " (cutoff:3.500A) Proline residue: K 125 - end of helix Processing helix chain 'K' and resid 139 through 162 Processing helix chain 'K' and resid 168 through 186 Processing sheet with id=AA1, first strand: chain 'E' and resid 33 through 36 Processing sheet with id=AA2, first strand: chain 'E' and resid 47 through 51 removed outlier: 3.992A pdb=" N ILE E 47 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 165 through 166 removed outlier: 5.242A pdb=" N PHE E 208 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE E 198 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU E 195 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL E 184 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY E 197 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE E 182 " --> pdb=" O GLY E 197 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N MET E 199 " --> pdb=" O ASN E 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 244 through 249 removed outlier: 5.262A pdb=" N LEU E 254 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU E 262 " --> pdb=" O ALA E 281 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 294 through 298 Processing sheet with id=AA6, first strand: chain 'E' and resid 355 through 363 removed outlier: 5.484A pdb=" N VAL E 357 " --> pdb=" O ASN E 374 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN E 374 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR E 359 " --> pdb=" O LEU E 372 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 355 through 363 removed outlier: 5.484A pdb=" N VAL E 357 " --> pdb=" O ASN E 374 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN E 374 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR E 359 " --> pdb=" O LEU E 372 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL E 385 " --> pdb=" O PRO E 400 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 411 through 416 removed outlier: 3.646A pdb=" N GLY E 413 " --> pdb=" O TYR E 426 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE E 430 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 451 through 456 removed outlier: 3.552A pdb=" N LYS E 453 " --> pdb=" O ILE E 466 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG E 471 " --> pdb=" O VAL E 467 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE E 472 " --> pdb=" O LEU E 485 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 494 through 497 Processing sheet with id=AB2, first strand: chain 'E' and resid 538 through 543 removed outlier: 4.334A pdb=" N ILE E 538 " --> pdb=" O HIS E 554 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR E 603 " --> pdb=" O ALA E 553 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N GLN E 602 " --> pdb=" O MET E 593 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N MET E 593 " --> pdb=" O GLN E 602 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER E 604 " --> pdb=" O VAL E 591 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL E 591 " --> pdb=" O SER E 604 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N HIS E 606 " --> pdb=" O LYS E 589 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS E 576 " --> pdb=" O ILE E 588 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 693 through 695 removed outlier: 7.109A pdb=" N LEU E 682 " --> pdb=" O ILE E 670 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE E 670 " --> pdb=" O LEU E 682 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR E 684 " --> pdb=" O PHE E 668 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE E 668 " --> pdb=" O THR E 684 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS E 658 " --> pdb=" O ILE E 670 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 722 through 725 Processing sheet with id=AB5, first strand: chain 'E' and resid 737 through 740 removed outlier: 6.456A pdb=" N LYS E 738 " --> pdb=" O LYS E 828 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY E 803 " --> pdb=" O SER E 829 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 737 through 740 removed outlier: 6.456A pdb=" N LYS E 738 " --> pdb=" O LYS E 828 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY E 803 " --> pdb=" O SER E 829 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 836 through 839 Processing sheet with id=AB8, first strand: chain 'E' and resid 864 through 866 removed outlier: 13.618A pdb=" N LYS E 942 " --> pdb=" O GLU E1044 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N GLN E1046 " --> pdb=" O LYS E 942 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N HIS E 944 " --> pdb=" O GLN E1046 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE E1045 " --> pdb=" O PHE E1028 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 950 through 954 removed outlier: 5.594A pdb=" N THR E 951 " --> pdb=" O ILE E1020 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE E1020 " --> pdb=" O THR E 951 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 46 through 52 removed outlier: 7.041A pdb=" N PHE F 104 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N LEU F 168 " --> pdb=" O PHE F 104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 199 through 202 removed outlier: 4.572A pdb=" N VAL F 182 " --> pdb=" O MET F 132 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL F 145 " --> pdb=" O TYR F 131 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU F 150 " --> pdb=" O ALA F 658 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER F 655 " --> pdb=" O LEU F 741 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 209 through 210 Processing sheet with id=AC4, first strand: chain 'F' and resid 222 through 223 Processing sheet with id=AC5, first strand: chain 'F' and resid 242 through 243 removed outlier: 7.012A pdb=" N TRP F 242 " --> pdb=" O ALA F 303 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA F 301 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE F 309 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA F 303 " --> pdb=" O THR F 307 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR F 307 " --> pdb=" O ALA F 303 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL F 316 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 345 through 350 Processing sheet with id=AC7, first strand: chain 'F' and resid 403 through 411 removed outlier: 5.493A pdb=" N ILE F 405 " --> pdb=" O LYS F 422 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS F 422 " --> pdb=" O ILE F 405 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP F 407 " --> pdb=" O LEU F 420 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE F 428 " --> pdb=" O ILE F 446 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN F 432 " --> pdb=" O ILE F 442 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE F 442 " --> pdb=" O ASN F 432 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN F 434 " --> pdb=" O LEU F 440 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU F 440 " --> pdb=" O ASN F 434 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 458 through 460 removed outlier: 5.045A pdb=" N ILE F 493 " --> pdb=" O LEU F 505 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 514 through 519 Processing sheet with id=AD1, first strand: chain 'F' and resid 572 through 580 removed outlier: 5.736A pdb=" N LEU F 574 " --> pdb=" O TYR F 589 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR F 589 " --> pdb=" O LEU F 574 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 617 through 622 Processing sheet with id=AD3, first strand: chain 'F' and resid 638 through 642 removed outlier: 3.837A pdb=" N THR F 765 " --> pdb=" O ILE F 642 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 662 through 663 Processing sheet with id=AD5, first strand: chain 'F' and resid 754 through 756 removed outlier: 6.538A pdb=" N PHE F 754 " --> pdb=" O PHE F 875 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 857 through 860 Processing sheet with id=AD7, first strand: chain 'F' and resid 882 through 886 Processing sheet with id=AD8, first strand: chain 'F' and resid 914 through 916 removed outlier: 3.501A pdb=" N HIS F1053 " --> pdb=" O PHE F 915 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU F1030 " --> pdb=" O VAL F 946 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL F 946 " --> pdb=" O LEU F1030 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N SER F1032 " --> pdb=" O LEU F 944 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU F 944 " --> pdb=" O SER F1032 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY F 949 " --> pdb=" O ARG F 957 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 979 through 980 Processing sheet with id=AE1, first strand: chain 'G' and resid 22 through 25 removed outlier: 7.028A pdb=" N ILE G 346 " --> pdb=" O GLU G 342 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 40 through 41 removed outlier: 3.806A pdb=" N ASP G 40 " --> pdb=" O VAL G 84 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.025A pdb=" N PHE G 43 " --> pdb=" O ILE G 95 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N SER G 97 " --> pdb=" O PHE G 43 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL G 109 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA G 98 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU G 107 " --> pdb=" O ALA G 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 50 through 53 Processing sheet with id=AE5, first strand: chain 'G' and resid 136 through 139 removed outlier: 4.644A pdb=" N ILE G 170 " --> pdb=" O MET G 183 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 194 through 201 removed outlier: 5.343A pdb=" N LEU G 195 " --> pdb=" O VAL G 212 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL G 212 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR G 221 " --> pdb=" O SER G 229 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER G 229 " --> pdb=" O TYR G 221 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 194 through 201 removed outlier: 5.343A pdb=" N LEU G 195 " --> pdb=" O VAL G 212 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL G 212 " --> pdb=" O LEU G 195 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 241 through 244 Processing sheet with id=AE9, first strand: chain 'G' and resid 280 through 283 removed outlier: 4.682A pdb=" N LYS G 326 " --> pdb=" O ILE G 276 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR G 323 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA G 304 " --> pdb=" O VAL G 296 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL G 296 " --> pdb=" O ALA G 304 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU G 306 " --> pdb=" O TYR G 294 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 386 through 390 removed outlier: 6.111A pdb=" N SER G 449 " --> pdb=" O PRO G 414 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS G 450 " --> pdb=" O PHE G 441 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 398 through 400 removed outlier: 6.554A pdb=" N PHE G 398 " --> pdb=" O SER G 504 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 512 through 515 removed outlier: 5.637A pdb=" N LYS G 587 " --> pdb=" O VAL G 591 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL G 591 " --> pdb=" O LYS G 587 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 537 through 539 Processing sheet with id=AF5, first strand: chain 'G' and resid 571 through 574 removed outlier: 6.181A pdb=" N ARG G 571 " --> pdb=" O TYR G 710 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N HIS G 712 " --> pdb=" O ARG G 571 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL G 573 " --> pdb=" O HIS G 712 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 610 through 612 Processing sheet with id=AF7, first strand: chain 'H' and resid 51 through 55 removed outlier: 4.179A pdb=" N THR H 98 " --> pdb=" O GLU H 90 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 80 through 82 Processing sheet with id=AF9, first strand: chain 'H' and resid 210 through 215 removed outlier: 5.841A pdb=" N PHE H 236 " --> pdb=" O ILE H 129 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 197 through 199 removed outlier: 3.862A pdb=" N LEU H 197 " --> pdb=" O THR H 192 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 258 through 259 Processing sheet with id=AG3, first strand: chain 'H' and resid 269 through 272 Processing sheet with id=AG4, first strand: chain 'H' and resid 316 through 321 removed outlier: 6.656A pdb=" N LEU H 329 " --> pdb=" O ARG H 317 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL H 319 " --> pdb=" O LEU H 327 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU H 327 " --> pdb=" O VAL H 319 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL H 334 " --> pdb=" O LEU H 345 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 358 through 360 removed outlier: 3.521A pdb=" N GLY H 358 " --> pdb=" O TRP H 383 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ALA H 390 " --> pdb=" O THR H 399 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR H 399 " --> pdb=" O ALA H 390 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 418 through 425 removed outlier: 5.831A pdb=" N VAL H 420 " --> pdb=" O SER H 437 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER H 437 " --> pdb=" O VAL H 420 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER H 422 " --> pdb=" O LEU H 435 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 418 through 425 removed outlier: 5.831A pdb=" N VAL H 420 " --> pdb=" O SER H 437 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER H 437 " --> pdb=" O VAL H 420 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER H 422 " --> pdb=" O LEU H 435 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 477 through 480 Processing sheet with id=AG9, first strand: chain 'H' and resid 527 through 532 Processing sheet with id=AH1, first strand: chain 'H' and resid 569 through 574 removed outlier: 4.126A pdb=" N LYS H 569 " --> pdb=" O TYR H 585 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 621 through 624 removed outlier: 3.516A pdb=" N ALA H 621 " --> pdb=" O VAL H 646 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE H 645 " --> pdb=" O LYS H 682 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 630 through 633 removed outlier: 6.707A pdb=" N TYR H 631 " --> pdb=" O ASP H 734 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 742 through 745 removed outlier: 3.895A pdb=" N LYS H 810 " --> pdb=" O LEU H 802 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 758 through 762 removed outlier: 4.095A pdb=" N ILE H 762 " --> pdb=" O LEU H 775 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU H 775 " --> pdb=" O ILE H 762 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 788 through 789 removed outlier: 6.080A pdb=" N LEU H 788 " --> pdb=" O GLU H 928 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 828 through 829 Processing sheet with id=AH8, first strand: chain 'L' and resid 504 through 506 Processing sheet with id=AH9, first strand: chain 'L' and resid 521 through 523 removed outlier: 5.376A pdb=" N CYS L 521 " --> pdb=" O CYS L 536 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N CYS L 536 " --> pdb=" O CYS L 521 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 634 through 635 removed outlier: 7.269A pdb=" N TYR L 634 " --> pdb=" O TRP L 647 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 48 through 50 removed outlier: 4.879A pdb=" N VAL J 48 " --> pdb=" O HIS J 57 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS J 57 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE J 60 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N THR J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 78 through 81 Processing sheet with id=AI4, first strand: chain 'I' and resid 43 through 45 2231 hydrogen bonds defined for protein. 6264 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: 24.10 Time building geometry restraints manager: 21.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 7496 1.27 - 1.41: 12831 1.41 - 1.55: 28294 1.55 - 1.69: 22 1.69 - 1.83: 416 Bond restraints: 49059 Sorted by residual: bond pdb=" C ILE E 807 " pdb=" O ILE E 807 " ideal model delta sigma weight residual 1.237 1.134 0.103 1.10e-02 8.26e+03 8.72e+01 bond pdb=" C ILE F 442 " pdb=" O ILE F 442 " ideal model delta sigma weight residual 1.233 1.142 0.091 1.09e-02 8.42e+03 7.02e+01 bond pdb=" C LYS E 999 " pdb=" O LYS E 999 " ideal model delta sigma weight residual 1.237 1.144 0.092 1.17e-02 7.31e+03 6.22e+01 bond pdb=" C TYR F 138 " pdb=" O TYR F 138 " ideal model delta sigma weight residual 1.237 1.144 0.093 1.19e-02 7.06e+03 6.09e+01 bond pdb=" C ASN F 498 " pdb=" O ASN F 498 " ideal model delta sigma weight residual 1.236 1.148 0.087 1.14e-02 7.69e+03 5.87e+01 ... (remaining 49054 not shown) Histogram of bond angle deviations from ideal: 95.87 - 103.72: 669 103.72 - 111.57: 22738 111.57 - 119.42: 18623 119.42 - 127.27: 24170 127.27 - 135.12: 550 Bond angle restraints: 66750 Sorted by residual: angle pdb=" N ILE A 471 " pdb=" CA ILE A 471 " pdb=" C ILE A 471 " ideal model delta sigma weight residual 112.83 102.95 9.88 9.90e-01 1.02e+00 9.95e+01 angle pdb=" C ASP E 655 " pdb=" N VAL E 656 " pdb=" CA VAL E 656 " ideal model delta sigma weight residual 121.96 133.30 -11.34 1.34e+00 5.57e-01 7.16e+01 angle pdb=" N PRO E 895 " pdb=" CA PRO E 895 " pdb=" C PRO E 895 " ideal model delta sigma weight residual 113.53 124.71 -11.18 1.39e+00 5.18e-01 6.47e+01 angle pdb=" N ASN L 486 " pdb=" CA ASN L 486 " pdb=" C ASN L 486 " ideal model delta sigma weight residual 111.28 102.53 8.75 1.09e+00 8.42e-01 6.45e+01 angle pdb=" C PHE B 222 " pdb=" N ARG B 223 " pdb=" CA ARG B 223 " ideal model delta sigma weight residual 120.44 130.61 -10.17 1.30e+00 5.92e-01 6.12e+01 ... (remaining 66745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 26083 17.99 - 35.98: 2186 35.98 - 53.97: 414 53.97 - 71.96: 92 71.96 - 89.95: 40 Dihedral angle restraints: 28815 sinusoidal: 11196 harmonic: 17619 Sorted by residual: dihedral pdb=" CB CYS L 497 " pdb=" SG CYS L 497 " pdb=" SG CYS L 517 " pdb=" CB CYS L 517 " ideal model delta sinusoidal sigma weight residual 93.00 168.57 -75.57 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS F 160 " pdb=" SG CYS F 160 " pdb=" SG CYS F 166 " pdb=" CB CYS F 166 " ideal model delta sinusoidal sigma weight residual 93.00 167.79 -74.79 1 1.00e+01 1.00e-02 7.08e+01 dihedral pdb=" CB CYS F 289 " pdb=" SG CYS F 289 " pdb=" SG CYS F 344 " pdb=" CB CYS F 344 " ideal model delta sinusoidal sigma weight residual -86.00 -159.28 73.28 1 1.00e+01 1.00e-02 6.84e+01 ... (remaining 28812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.304: 7759 0.304 - 0.608: 65 0.608 - 0.912: 7 0.912 - 1.216: 3 1.216 - 1.520: 3 Chirality restraints: 7837 Sorted by residual: chirality pdb=" C1 BMA U 3 " pdb=" O4 NAG U 2 " pdb=" C2 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.13e+01 chirality pdb=" C1 NAG G 902 " pdb=" ND2 ASN G 535 " pdb=" C2 NAG G 902 " pdb=" O5 NAG G 902 " both_signs ideal model delta sigma weight residual False -2.40 -0.88 -1.52 2.00e-01 2.50e+01 5.78e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.09e+01 ... (remaining 7834 not shown) Planarity restraints: 8268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 920 " 0.160 2.00e-02 2.50e+03 3.74e-01 1.75e+03 pdb=" CG ASN H 920 " -0.115 2.00e-02 2.50e+03 pdb=" OD1 ASN H 920 " 0.197 2.00e-02 2.50e+03 pdb=" ND2 ASN H 920 " -0.666 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " 0.423 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 227 " 0.148 2.00e-02 2.50e+03 2.49e-01 7.74e+02 pdb=" CG ASN G 227 " -0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN G 227 " 0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN G 227 " -0.430 2.00e-02 2.50e+03 pdb=" C1 NAG G 901 " 0.305 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN H 502 " -0.129 2.00e-02 2.50e+03 1.68e-01 3.54e+02 pdb=" CG ASN H 502 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN H 502 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN H 502 " 0.277 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " -0.210 2.00e-02 2.50e+03 ... (remaining 8265 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.11: 36 2.11 - 2.81: 14156 2.81 - 3.51: 65397 3.51 - 4.20: 108987 4.20 - 4.90: 191471 Nonbonded interactions: 380047 Sorted by model distance: nonbonded pdb=" OD1 ASN F 402 " pdb=" C1 NAG F1201 " model vdw 1.419 2.776 nonbonded pdb=" O TRP G 579 " pdb=" CG2 ILE G 678 " model vdw 1.795 3.460 nonbonded pdb=" O GLU L 476 " pdb=" O ASP L 477 " model vdw 1.809 3.040 nonbonded pdb=" O ASP F 266 " pdb=" OG SER F 267 " model vdw 1.849 2.440 nonbonded pdb=" OD1 ASP L 547 " pdb=" N ASP L 548 " model vdw 1.876 2.520 ... (remaining 380042 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 'O' selection = chain 'Z' } ncs_group { reference = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'a' selection = chain 'd' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'W' selection = chain 'b' } ncs_group { reference = chain 'Y' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 262 5.16 5 Na 2 4.78 5 C 31144 2.51 5 N 7669 2.21 5 O 8797 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 17.470 Check model and map are aligned: 0.750 Convert atoms to be neutral: 0.430 Process input model: 124.370 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 : 0.008 0.103 49059 Z= 0.525 Angle : 1.117 12.681 66750 Z= 0.718 Chirality : 0.084 1.520 7837 Planarity : 0.008 0.157 8243 Dihedral : 14.165 89.951 17334 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 23.48 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.05 % Favored : 93.22 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.60 % 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: -0.99 (0.10), residues: 5929 helix: 0.02 (0.12), residues: 1968 sheet: 0.09 (0.14), residues: 1283 loop : -1.52 (0.11), residues: 2678 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 944 time to evaluate : 5.816 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 148 outliers final: 44 residues processed: 1067 average time/residue: 1.3575 time to fit residues: 1857.7000 Evaluate side-chains 571 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 527 time to evaluate : 5.218 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 39 residues processed: 6 average time/residue: 0.5650 time to fit residues: 13.0418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 501 optimal weight: 3.9990 chunk 450 optimal weight: 0.6980 chunk 249 optimal weight: 0.9990 chunk 153 optimal weight: 0.0370 chunk 303 optimal weight: 0.2980 chunk 240 optimal weight: 0.9980 chunk 465 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 283 optimal weight: 0.6980 chunk 346 optimal weight: 0.8980 chunk 539 optimal weight: 20.0000 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN D 185 GLN D 236 GLN E 45 HIS E 449 HIS E 606 HIS ** E 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 719 GLN ** E 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 839 HIS E 862 ASN E 876 HIS E 886 ASN E 928 GLN E 989 HIS E1000 HIS F 67 GLN F 69 HIS F 119 HIS F 130 ASN ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 427 GLN F 498 ASN F 622 GLN F 632 HIS F 649 HIS F 671 ASN F 673 ASN F 786 ASN F1018 GLN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 ASN G 443 ASN G 465 ASN G 517 ASN G 588 ASN G 644 ASN ** G 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 607 GLN H 670 ASN H 707 ASN H 825 ASN ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.138 49059 Z= 0.222 Angle : 0.699 13.237 66750 Z= 0.363 Chirality : 0.047 0.543 7837 Planarity : 0.005 0.089 8243 Dihedral : 5.613 94.285 6911 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.94 % Favored : 94.75 % Rotamer Outliers : 3.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.56 (0.11), residues: 5929 helix: 0.62 (0.11), residues: 2066 sheet: 0.16 (0.14), residues: 1290 loop : -1.46 (0.12), residues: 2573 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 592 time to evaluate : 5.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 190 outliers final: 65 residues processed: 718 average time/residue: 1.2593 time to fit residues: 1186.3475 Evaluate side-chains 556 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 491 time to evaluate : 5.342 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 52 residues processed: 14 average time/residue: 0.7824 time to fit residues: 23.8023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 299 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 448 optimal weight: 0.0270 chunk 367 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 540 optimal weight: 6.9990 chunk 583 optimal weight: 7.9990 chunk 481 optimal weight: 9.9990 chunk 535 optimal weight: 30.0000 chunk 184 optimal weight: 7.9990 chunk 433 optimal weight: 1.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN D 81 ASN E 450 HIS ** E 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 725 GLN E 889 HIS F 312 GLN F 313 ASN ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 622 GLN F 679 GLN G 220 HIS G 228 HIS ** G 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 ASN H 517 ASN H 607 GLN H 670 ASN H 825 ASN L 158 ASN L 247 HIS L 426 HIS L 475 ASN ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 582 ASN M 44 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.085 49059 Z= 0.460 Angle : 0.792 16.380 66750 Z= 0.408 Chirality : 0.054 1.371 7837 Planarity : 0.005 0.068 8243 Dihedral : 5.842 70.470 6911 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.14 % Favored : 93.64 % Rotamer Outliers : 4.99 % 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: -0.64 (0.11), residues: 5929 helix: 0.69 (0.11), residues: 2085 sheet: 0.05 (0.14), residues: 1298 loop : -1.62 (0.12), residues: 2546 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 552 time to evaluate : 5.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 248 outliers final: 101 residues processed: 729 average time/residue: 1.2731 time to fit residues: 1215.6530 Evaluate side-chains 593 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 492 time to evaluate : 5.040 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 78 residues processed: 25 average time/residue: 0.8914 time to fit residues: 39.2815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 533 optimal weight: 30.0000 chunk 406 optimal weight: 0.6980 chunk 280 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 362 optimal weight: 3.9990 chunk 542 optimal weight: 40.0000 chunk 574 optimal weight: 6.9990 chunk 283 optimal weight: 0.6980 chunk 513 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 HIS A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN D 185 GLN ** E 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN G 228 HIS G 290 ASN G 588 ASN ** G 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS H 233 GLN H 469 GLN H 607 GLN H 670 ASN L 226 GLN L 364 ASN L 426 HIS L 475 ASN ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.093 49059 Z= 0.240 Angle : 0.655 12.570 66750 Z= 0.337 Chirality : 0.047 0.914 7837 Planarity : 0.004 0.053 8243 Dihedral : 5.421 63.587 6911 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.36 % Favored : 94.43 % Rotamer Outliers : 4.99 % 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: -0.43 (0.11), residues: 5929 helix: 0.98 (0.11), residues: 2077 sheet: 0.06 (0.14), residues: 1294 loop : -1.54 (0.12), residues: 2558 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 535 time to evaluate : 5.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 248 outliers final: 114 residues processed: 709 average time/residue: 1.2554 time to fit residues: 1187.3623 Evaluate side-chains 591 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 477 time to evaluate : 5.380 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 90 residues processed: 25 average time/residue: 0.7727 time to fit residues: 37.5072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 478 optimal weight: 8.9990 chunk 325 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 427 optimal weight: 0.6980 chunk 236 optimal weight: 2.9990 chunk 489 optimal weight: 5.9990 chunk 396 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 293 optimal weight: 0.9980 chunk 515 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN D 151 GLN D 185 GLN ** E 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 709 GLN ** F 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 HIS G 228 HIS G 644 ASN ** G 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN H 495 HIS H 670 ASN ** L 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 49059 Z= 0.303 Angle : 0.681 16.499 66750 Z= 0.347 Chirality : 0.047 0.878 7837 Planarity : 0.004 0.056 8243 Dihedral : 5.389 55.835 6911 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.90 % Favored : 93.93 % Rotamer Outliers : 4.93 % 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: -0.41 (0.11), residues: 5929 helix: 1.08 (0.11), residues: 2078 sheet: 0.04 (0.14), residues: 1280 loop : -1.59 (0.12), residues: 2571 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 509 time to evaluate : 5.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 245 outliers final: 136 residues processed: 693 average time/residue: 1.2006 time to fit residues: 1115.1921 Evaluate side-chains 630 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 494 time to evaluate : 5.613 Switching outliers to nearest non-outliers outliers start: 136 outliers final: 112 residues processed: 26 average time/residue: 0.8385 time to fit residues: 39.9536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 193 optimal weight: 5.9990 chunk 517 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 337 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 574 optimal weight: 0.0020 chunk 477 optimal weight: 40.0000 chunk 266 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 301 optimal weight: 0.8980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN C 63 ASN C 261 ASN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 899 ASN E 944 HIS ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 HIS G 588 ASN G 702 ASN ** G 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 607 GLN H 670 ASN L 426 HIS ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 49059 Z= 0.189 Angle : 0.621 14.212 66750 Z= 0.316 Chirality : 0.045 0.779 7837 Planarity : 0.004 0.055 8243 Dihedral : 5.112 50.741 6911 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.35 % Favored : 94.48 % Rotamer Outliers : 4.27 % 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 (0.11), residues: 5929 helix: 1.25 (0.11), residues: 2080 sheet: 0.12 (0.14), residues: 1264 loop : -1.49 (0.12), residues: 2585 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 528 time to evaluate : 5.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 212 outliers final: 130 residues processed: 693 average time/residue: 1.2826 time to fit residues: 1184.5577 Evaluate side-chains 621 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 491 time to evaluate : 5.723 Switching outliers to nearest non-outliers outliers start: 130 outliers final: 110 residues processed: 23 average time/residue: 0.9225 time to fit residues: 38.8288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 554 optimal weight: 0.0010 chunk 64 optimal weight: 0.0970 chunk 327 optimal weight: 0.7980 chunk 419 optimal weight: 4.9990 chunk 325 optimal weight: 4.9990 chunk 483 optimal weight: 10.0000 chunk 320 optimal weight: 0.0030 chunk 572 optimal weight: 0.9990 chunk 358 optimal weight: 0.9990 chunk 349 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN ** E 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 290 ASN G 702 ASN H 670 ASN L 475 ASN ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 49059 Z= 0.166 Angle : 0.618 15.032 66750 Z= 0.313 Chirality : 0.045 0.753 7837 Planarity : 0.004 0.053 8243 Dihedral : 4.906 48.237 6911 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.40 % Favored : 94.45 % Rotamer Outliers : 3.80 % 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: -0.14 (0.11), residues: 5929 helix: 1.33 (0.11), residues: 2096 sheet: 0.19 (0.14), residues: 1276 loop : -1.47 (0.12), residues: 2557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 523 time to evaluate : 5.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 189 outliers final: 115 residues processed: 671 average time/residue: 1.2808 time to fit residues: 1144.6329 Evaluate side-chains 613 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 498 time to evaluate : 5.443 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 102 residues processed: 15 average time/residue: 0.8837 time to fit residues: 27.0764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 354 optimal weight: 0.5980 chunk 228 optimal weight: 0.9980 chunk 341 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 363 optimal weight: 6.9990 chunk 390 optimal weight: 0.3980 chunk 283 optimal weight: 1.9990 chunk 53 optimal weight: 0.0040 chunk 450 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN A 545 ASN A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN C 63 ASN ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN D 185 GLN ** E 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 516 GLN G 702 ASN H 670 ASN ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 49059 Z= 0.178 Angle : 0.615 14.039 66750 Z= 0.311 Chirality : 0.045 0.764 7837 Planarity : 0.004 0.121 8243 Dihedral : 4.879 47.652 6911 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.33 % Favored : 94.54 % Rotamer Outliers : 3.42 % 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: -0.05 (0.11), residues: 5929 helix: 1.42 (0.12), residues: 2093 sheet: 0.22 (0.14), residues: 1281 loop : -1.43 (0.12), residues: 2555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 517 time to evaluate : 5.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 170 outliers final: 116 residues processed: 648 average time/residue: 1.3058 time to fit residues: 1123.5707 Evaluate side-chains 607 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 491 time to evaluate : 5.504 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 100 residues processed: 18 average time/residue: 0.7771 time to fit residues: 29.5658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 520 optimal weight: 8.9990 chunk 548 optimal weight: 50.0000 chunk 500 optimal weight: 8.9990 chunk 533 optimal weight: 9.9990 chunk 321 optimal weight: 0.7980 chunk 232 optimal weight: 0.5980 chunk 418 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 482 optimal weight: 30.0000 chunk 504 optimal weight: 3.9990 chunk 531 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN D 151 GLN D 185 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN ** F 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 702 ASN H 607 GLN H 670 ASN ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 49059 Z= 0.365 Angle : 0.715 14.119 66750 Z= 0.360 Chirality : 0.048 0.884 7837 Planarity : 0.004 0.064 8243 Dihedral : 5.245 46.994 6911 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.97 % Favored : 93.89 % Rotamer Outliers : 3.32 % 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 (0.11), residues: 5929 helix: 1.35 (0.11), residues: 2097 sheet: 0.09 (0.14), residues: 1271 loop : -1.54 (0.12), residues: 2561 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 506 time to evaluate : 5.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 115 residues processed: 638 average time/residue: 1.3037 time to fit residues: 1110.7710 Evaluate side-chains 603 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 488 time to evaluate : 5.362 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 103 residues processed: 14 average time/residue: 1.1122 time to fit residues: 29.2386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 350 optimal weight: 0.8980 chunk 564 optimal weight: 50.0000 chunk 344 optimal weight: 3.9990 chunk 267 optimal weight: 0.8980 chunk 392 optimal weight: 0.6980 chunk 591 optimal weight: 8.9990 chunk 544 optimal weight: 0.8980 chunk 471 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 363 optimal weight: 9.9990 chunk 288 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN D 185 GLN ** E 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 709 GLN ** F 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 607 GLN H 670 ASN ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 49059 Z= 0.207 Angle : 0.661 13.787 66750 Z= 0.332 Chirality : 0.045 0.799 7837 Planarity : 0.004 0.068 8243 Dihedral : 5.070 43.647 6911 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.62 % Favored : 94.23 % Rotamer Outliers : 2.64 % 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: -0.09 (0.11), residues: 5929 helix: 1.45 (0.12), residues: 2089 sheet: 0.19 (0.14), residues: 1281 loop : -1.51 (0.12), residues: 2559 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11858 Ramachandran restraints generated. 5929 Oldfield, 0 Emsley, 5929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 512 time to evaluate : 5.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 104 residues processed: 628 average time/residue: 1.3451 time to fit residues: 1129.8964 Evaluate side-chains 592 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 488 time to evaluate : 5.472 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 98 residues processed: 8 average time/residue: 0.7430 time to fit residues: 17.0625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 374 optimal weight: 4.9990 chunk 501 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 434 optimal weight: 0.4980 chunk 69 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 471 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 484 optimal weight: 30.0000 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN D 185 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 702 ASN G 746 GLN H 607 GLN H 670 ASN ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.190513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.128535 restraints weight = 68464.989| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.51 r_work: 0.3274 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 49059 Z= 0.347 Angle : 0.723 14.178 66750 Z= 0.361 Chirality : 0.048 0.884 7837 Planarity : 0.005 0.073 8243 Dihedral : 5.284 42.692 6911 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.19 % Favored : 93.62 % Rotamer Outliers : 2.78 % 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: -0.21 (0.11), residues: 5929 helix: 1.39 (0.11), residues: 2096 sheet: 0.05 (0.14), residues: 1252 loop : -1.57 (0.12), residues: 2581 =============================================================================== Job complete usr+sys time: 19200.76 seconds wall clock time: 338 minutes 51.14 seconds (20331.14 seconds total)