Starting phenix.real_space_refine on Sun Feb 25 01:47:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeb_31076/02_2024/7eeb_31076_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeb_31076/02_2024/7eeb_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_31076/02_2024/7eeb_31076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeb_31076/02_2024/7eeb_31076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeb_31076/02_2024/7eeb_31076_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeb_31076/02_2024/7eeb_31076_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 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. 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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 21 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 dihedrals: 6 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: 9 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: 9 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 dihedrals: 6 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 dihedrals: 6 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: 9 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 dihedrals: 6 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: 9 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 dihedrals: 6 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: 15 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: 21 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 dihedrals: 6 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: 9 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: 15 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 3 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 dihedrals: 9 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 23.31, per 1000 atoms: 0.49 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: 18.46 Conformation dependent library (CDL) restraints added in 9.3 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... running ksdssp... Secondary structure from input PDB file: 156 helices and 68 sheets defined 34.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.97 Creating SS restraints... Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 353 through 372 removed outlier: 4.325A pdb=" N THR A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 412 removed outlier: 4.430A pdb=" N TRP A 382 " --> pdb=" O ARG A 379 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 383 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET A 385 " --> pdb=" O TRP A 382 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY A 407 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A 408 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 410 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 434 Processing helix chain 'A' and resid 440 through 443 No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 446 through 469 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) removed outlier: 3.919A pdb=" N ARG A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA A 459 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG A 461 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) 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 476 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 516 through 519 No H-bonds generated for 'chain 'A' and resid 516 through 519' Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 538 through 548 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 551 through 567 Proline residue: A 555 - end of helix removed outlier: 4.118A pdb=" N TYR A 565 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE A 566 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A 567 " --> pdb=" O GLN A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 593 Processing helix chain 'B' and resid 96 through 104 removed outlier: 3.612A pdb=" N ASP B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 128 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 138 through 165 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 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 174 through 195 Proline residue: B 189 - end of helix Processing helix chain 'B' and resid 202 through 221 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) removed outlier: 5.420A pdb=" N ARG B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL B 212 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG B 214 " --> pdb=" O CYS B 210 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 216 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LYS B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) 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) Processing helix chain 'B' and resid 225 through 238 Processing helix chain 'B' and resid 240 through 260 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 281 through 292 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 315 through 325 Processing helix chain 'B' and resid 329 through 373 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 47 Processing helix chain 'C' and resid 50 through 71 removed outlier: 3.864A pdb=" N THR C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 80 through 103 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 113 through 133 Proline residue: C 128 - end of helix Processing helix chain 'C' and resid 142 through 158 removed outlier: 4.121A pdb=" N GLN C 149 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N SER C 150 " --> pdb=" O ASP C 146 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ARG C 152 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 199 removed outlier: 4.918A pdb=" N THR C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL C 174 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TYR C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 removed outlier: 4.284A pdb=" N PHE C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 237 Processing helix chain 'C' and resid 244 through 255 Processing helix chain 'C' and resid 260 through 314 removed outlier: 3.977A pdb=" N GLY C 265 " --> pdb=" O ASN C 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 65 removed outlier: 4.558A pdb=" N ILE D 56 " --> pdb=" O VAL D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 88 Processing helix chain 'D' and resid 91 through 96 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) No H-bonds generated for 'chain 'D' and resid 91 through 96' Processing helix chain 'D' and resid 98 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 124 through 128 Processing helix chain 'D' and resid 132 through 148 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 155 through 172 Proline residue: D 160 - end of helix removed outlier: 3.658A pdb=" N VAL D 163 " --> pdb=" O TYR D 159 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL D 167 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N HIS D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA D 172 " --> pdb=" O HIS D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 212 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 223 through 235 Processing helix chain 'D' and resid 239 through 247 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 254 through 270 removed outlier: 3.842A pdb=" N GLY D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 291 Processing helix chain 'E' and resid 73 through 79 Processing helix chain 'E' and resid 116 through 118 No H-bonds generated for 'chain 'E' and resid 116 through 118' Processing helix chain 'E' and resid 157 through 160 No H-bonds generated for 'chain 'E' and resid 157 through 160' Processing helix chain 'E' and resid 173 through 178 Proline residue: E 177 - end of helix Processing helix chain 'E' and resid 228 through 234 removed outlier: 3.637A pdb=" N GLU E 234 " --> pdb=" O ILE E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 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 389 through 391 No H-bonds generated for 'chain 'E' and resid 389 through 391' Processing helix chain 'E' and resid 561 through 567 removed outlier: 5.279A pdb=" N TRP E 565 " --> pdb=" O ASN E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 573 No H-bonds generated for 'chain 'E' and resid 571 through 573' Processing helix chain 'E' and resid 622 through 624 No H-bonds generated for 'chain 'E' and resid 622 through 624' Processing helix chain 'E' and resid 686 through 688 No H-bonds generated for 'chain 'E' and resid 686 through 688' Processing helix chain 'E' and resid 697 through 699 No H-bonds generated for 'chain 'E' and resid 697 through 699' Processing helix chain 'E' and resid 847 through 852 Processing helix chain 'E' and resid 903 through 906 No H-bonds generated for 'chain 'E' and resid 903 through 906' Processing helix chain 'E' and resid 926 through 930 Processing helix chain 'E' and resid 937 through 939 No H-bonds generated for 'chain 'E' and resid 937 through 939' Processing helix chain 'E' and resid 998 through 1006 Proline residue: E1004 - end of helix Processing helix chain 'E' and resid 1060 through 1085 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 76 through 81 Processing helix chain 'F' and resid 111 through 121 Processing helix chain 'F' and resid 230 through 234 Processing helix chain 'F' and resid 394 through 396 No H-bonds generated for 'chain 'F' and resid 394 through 396' Processing helix chain 'F' and resid 413 through 415 No H-bonds generated for 'chain 'F' and resid 413 through 415' Processing helix chain 'F' and resid 551 through 562 Processing helix chain 'F' and resid 605 through 610 Processing helix chain 'F' and resid 647 through 651 Processing helix chain 'F' and resid 672 through 693 removed outlier: 4.538A pdb=" N ASP F 693 " --> pdb=" O HIS F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 703 through 723 removed outlier: 4.719A pdb=" N GLN F 709 " --> pdb=" O ARG F 706 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS F 710 " --> pdb=" O TRP F 707 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS F 715 " --> pdb=" O THR F 712 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP F 716 " --> pdb=" O LYS F 713 " (cutoff:3.500A) Processing helix chain 'F' and resid 735 through 737 No H-bonds generated for 'chain 'F' and resid 735 through 737' Processing helix chain 'F' and resid 777 through 779 No H-bonds generated for 'chain 'F' and resid 777 through 779' Processing helix chain 'F' and resid 787 through 790 No H-bonds generated for 'chain 'F' and resid 787 through 790' Processing helix chain 'F' and resid 800 through 802 No H-bonds generated for 'chain 'F' and resid 800 through 802' Processing helix chain 'F' and resid 836 through 839 removed outlier: 4.044A pdb=" N ASN F 839 " --> pdb=" O ILE F 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 836 through 839' Processing helix chain 'F' and resid 888 through 898 Processing helix chain 'F' and resid 961 through 968 Processing helix chain 'F' and resid 988 through 990 No H-bonds generated for 'chain 'F' and resid 988 through 990' Processing helix chain 'F' and resid 1059 through 1084 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 147 through 154 Processing helix chain 'G' and resid 185 through 188 Processing helix chain 'G' and resid 286 through 289 No H-bonds generated for 'chain 'G' and resid 286 through 289' Processing helix chain 'G' and resid 370 through 373 No H-bonds generated for 'chain 'G' and resid 370 through 373' Processing helix chain 'G' and resid 460 through 463 No H-bonds generated for 'chain 'G' and resid 460 through 463' Processing helix chain 'G' and resid 468 through 471 No H-bonds generated for 'chain 'G' and resid 468 through 471' Processing helix chain 'G' and resid 529 through 533 Processing helix chain 'G' and resid 564 through 567 No H-bonds generated for 'chain 'G' and resid 564 through 567' Processing helix chain 'G' and resid 725 through 747 removed outlier: 3.869A pdb=" N TRP G 738 " --> pdb=" O LEU G 734 " (cutoff:3.500A) Proline residue: G 744 - end of helix Processing helix chain 'H' and resid 160 through 163 No H-bonds generated for 'chain 'H' and resid 160 through 163' Processing helix chain 'H' and resid 172 through 183 Processing helix chain 'H' and resid 310 through 315 Processing helix chain 'H' and resid 367 through 372 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 409 Processing helix chain 'H' and resid 518 through 521 No H-bonds generated for 'chain 'H' and resid 518 through 521' Processing helix chain 'H' and resid 602 through 613 Processing helix chain 'H' and resid 700 through 706 Processing helix chain 'H' and resid 833 through 836 No H-bonds generated for 'chain 'H' and resid 833 through 836' Processing helix chain 'H' and resid 845 through 851 Processing helix chain 'H' and resid 857 through 860 No H-bonds generated for 'chain 'H' and resid 857 through 860' Processing helix chain 'H' and resid 869 through 871 No H-bonds generated for 'chain 'H' and resid 869 through 871' Processing helix chain 'H' and resid 938 through 966 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 85 through 89 Processing helix chain 'L' and resid 93 through 124 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 129 through 147 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) Processing helix chain 'L' and resid 149 through 156 removed outlier: 3.786A pdb=" N LYS L 156 " --> pdb=" O HIS L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 183 removed outlier: 3.587A pdb=" N MET L 175 " --> pdb=" O GLY L 171 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA L 178 " --> pdb=" O SER L 174 " (cutoff:3.500A) Proline residue: L 180 - end of helix Processing helix chain 'L' and resid 204 through 206 No H-bonds generated for 'chain 'L' and resid 204 through 206' Processing helix chain 'L' and resid 216 through 247 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 250 through 279 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 290 through 323 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 329 through 339 Processing helix chain 'L' and resid 358 through 370 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 372 through 401 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 407 through 415 removed outlier: 3.596A pdb=" N THR L 414 " --> pdb=" O ALA L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 418 through 436 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 440 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 490 through 494 Processing helix chain 'L' and resid 565 through 594 Proline residue: L 568 - end of helix removed outlier: 3.893A pdb=" N PHE L 571 " --> pdb=" O PRO L 568 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA L 572 " --> pdb=" O LEU L 569 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER L 576 " --> pdb=" O PHE L 573 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA L 577 " --> pdb=" O TYR L 574 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL L 579 " --> pdb=" O SER L 576 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER L 585 " --> pdb=" O ASN L 582 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE L 586 " --> pdb=" O MET L 583 " (cutoff:3.500A) Proline residue: L 587 - end of helix removed outlier: 3.634A pdb=" N SER L 590 " --> pdb=" O PRO L 587 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU L 593 " --> pdb=" O SER L 590 " (cutoff:3.500A) Processing helix chain 'L' and resid 598 through 600 No H-bonds generated for 'chain 'L' and resid 598 through 600' Processing helix chain 'L' and resid 602 through 613 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) Processing helix chain 'L' and resid 617 through 631 Proline residue: L 621 - end of helix removed outlier: 3.711A pdb=" N ALA L 631 " --> pdb=" O SER L 627 " (cutoff:3.500A) Processing helix chain 'L' and resid 653 through 688 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 16 removed outlier: 3.640A pdb=" N ILE J 10 " --> pdb=" O CYS J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 40 removed outlier: 4.145A pdb=" N GLY J 34 " --> pdb=" O MET J 31 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET J 38 " --> pdb=" O LEU J 35 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU J 39 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 123 removed outlier: 3.805A pdb=" N GLY J 117 " --> pdb=" O MET J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 132 No H-bonds generated for 'chain 'J' and resid 129 through 132' Processing helix chain 'J' and resid 150 through 159 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 9 removed outlier: 3.869A pdb=" N ILE M 7 " --> pdb=" O TRP M 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 41 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 54 through 78 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 81 through 101 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 103 through 107 Processing helix chain 'N' and resid 12 through 29 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 5 through 17 Processing helix chain 'I' and resid 25 through 36 Processing helix chain 'I' and resid 46 through 56 Processing helix chain 'I' and resid 61 through 71 Processing helix chain 'I' and resid 81 through 91 Processing helix chain 'I' and resid 97 through 105 removed outlier: 3.789A pdb=" N HIS I 101 " --> pdb=" O HIS I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 133 Processing helix chain 'I' and resid 138 through 148 Processing helix chain 'I' and resid 158 through 173 Processing helix chain 'K' and resid 43 through 46 No H-bonds generated for 'chain 'K' and resid 43 through 46' Processing helix chain 'K' and resid 57 through 74 Processing helix chain 'K' and resid 78 through 93 Processing helix chain 'K' and resid 101 through 111 removed outlier: 3.526A pdb=" N SER K 106 " --> pdb=" O HIS K 103 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR K 108 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 134 Proline residue: K 125 - end of helix Processing helix chain 'K' and resid 140 through 161 Processing helix chain 'K' and resid 169 through 185 Processing sheet with id= A, first strand: chain 'E' and resid 33 through 36 Processing sheet with id= B, 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= C, first strand: chain 'E' and resid 222 through 226 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) Processing sheet with id= D, first strand: chain 'E' and resid 278 through 281 removed outlier: 4.533A pdb=" N LEU E 262 " --> pdb=" O ALA E 281 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU E 254 " --> pdb=" O SER E 265 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 294 through 298 Processing sheet with id= F, first strand: chain 'E' and resid 381 through 387 removed outlier: 3.802A pdb=" N THR E 359 " --> pdb=" O LEU E 372 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN E 374 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL E 357 " --> pdb=" O ASN E 374 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 411 through 416 removed outlier: 6.856A pdb=" N TYR E 426 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET E 414 " --> pdb=" O TYR E 424 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR E 424 " --> pdb=" O MET E 414 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL E 432 " --> pdb=" O MET E 442 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N MET E 442 " --> pdb=" O VAL E 432 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 451 through 456 removed outlier: 7.026A pdb=" N ILE E 466 " --> pdb=" O THR E 452 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR E 454 " --> pdb=" O VAL E 464 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL E 464 " --> pdb=" O THR E 454 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN E 456 " --> pdb=" O ASP E 462 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP E 462 " --> pdb=" O ASN E 456 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG E 471 " --> pdb=" O VAL E 467 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY E 486 " --> pdb=" O ILE E 472 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N THR E 474 " --> pdb=" O GLU E 484 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLU E 484 " --> pdb=" O THR E 474 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 494 through 497 Processing sheet with id= J, 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: 6.468A pdb=" N GLU E 608 " --> pdb=" O ILE E 588 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE E 588 " --> pdb=" O GLU E 608 " (cutoff:3.500A) Processing sheet with id= K, 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= L, first strand: chain 'E' and resid 722 through 725 Processing sheet with id= M, first strand: chain 'E' and resid 737 through 740 removed outlier: 8.054A pdb=" N LYS E 738 " --> pdb=" O LEU E 824 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR E 826 " --> pdb=" O LYS E 738 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE E 740 " --> pdb=" O THR E 826 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYS E 828 " --> pdb=" O ILE E 740 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY E 803 " --> pdb=" O SER E 829 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 836 through 839 Processing sheet with id= O, first strand: chain 'E' and resid 864 through 866 Processing sheet with id= P, first strand: chain 'E' and resid 974 through 978 removed outlier: 3.677A pdb=" N PHE E1045 " --> pdb=" O PHE E1028 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 985 through 988 Processing sheet with id= R, 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= S, first strand: chain 'F' and resid 738 through 741 removed outlier: 4.565A pdb=" N SER F 655 " --> pdb=" O LEU F 741 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN F 144 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N TYR F 656 " --> pdb=" O ASN F 144 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN F 146 " --> pdb=" O TYR F 656 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ALA F 658 " --> pdb=" O GLN F 146 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU F 148 " --> pdb=" O ALA F 658 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL F 145 " --> pdb=" O TYR F 131 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL F 182 " --> pdb=" O MET F 132 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 250 through 253 Processing sheet with id= U, first strand: chain 'F' and resid 302 through 304 removed outlier: 4.293A pdb=" N VAL F 316 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 382 through 387 Processing sheet with id= W, first strand: chain 'F' and resid 403 through 411 removed outlier: 6.622A pdb=" N LEU F 420 " --> pdb=" O ASP F 406 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA F 408 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU F 418 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TYR F 410 " --> pdb=" O ASN F 416 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN F 416 " --> pdb=" O TYR F 410 " (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= X, first strand: chain 'F' and resid 458 through 460 Processing sheet with id= Y, first strand: chain 'F' and resid 493 through 496 Processing sheet with id= Z, first strand: chain 'F' and resid 544 through 546 Processing sheet with id= AA, first strand: chain 'F' and resid 597 through 602 removed outlier: 6.369A pdb=" N TYR F 589 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU F 574 " --> pdb=" O TYR F 589 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 617 through 622 Processing sheet with id= AC, 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= AD, first strand: chain 'F' and resid 753 through 756 removed outlier: 8.616A pdb=" N PHE F 754 " --> pdb=" O VAL F 871 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU F 756 " --> pdb=" O PRO F 873 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE F 875 " --> pdb=" O LEU F 756 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 857 through 860 Processing sheet with id= AF, first strand: chain 'F' and resid 882 through 886 Processing sheet with id= AG, first strand: chain 'F' and resid 914 through 916 removed outlier: 9.024A pdb=" N PHE F 915 " --> pdb=" O ILE F1049 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N HIS F1051 " --> 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) Processing sheet with id= AH, first strand: chain 'G' and resid 22 through 25 removed outlier: 3.662A pdb=" N ASP G 343 " --> pdb=" O ILE G 346 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN G 348 " --> pdb=" O PHE G 341 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N PHE G 341 " --> pdb=" O GLN G 348 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU G 350 " --> pdb=" O ILE G 339 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ILE G 339 " --> pdb=" O LEU G 350 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR G 337 " --> pdb=" O PRO G 352 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 50 through 53 Processing sheet with id= AJ, first strand: chain 'G' and resid 124 through 126 removed outlier: 3.903A pdb=" N SER G 97 " --> pdb=" O VAL G 109 " (cutoff:3.500A) Processing sheet with id= AK, 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= AL, first strand: chain 'G' and resid 217 through 221 removed outlier: 6.633A pdb=" N VAL G 212 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU G 195 " --> pdb=" O VAL G 212 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 241 through 244 Processing sheet with id= AN, 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) Processing sheet with id= AO, first strand: chain 'G' and resid 398 through 400 Processing sheet with id= AP, first strand: chain 'G' and resid 432 through 440 Processing sheet with id= AQ, 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= AR, first strand: chain 'G' and resid 537 through 539 Processing sheet with id= AS, first strand: chain 'G' and resid 571 through 574 Processing sheet with id= AT, first strand: chain 'G' and resid 610 through 612 Processing sheet with id= AU, 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= AV, first strand: chain 'H' and resid 80 through 82 Processing sheet with id= AW, first strand: chain 'H' and resid 105 through 109 Processing sheet with id= AX, first strand: chain 'H' and resid 210 through 215 removed outlier: 6.998A pdb=" N PHE H 236 " --> pdb=" O CYS H 130 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU H 132 " --> pdb=" O PHE H 236 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA H 238 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR H 134 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'H' and resid 197 through 200 removed outlier: 3.862A pdb=" N LEU H 197 " --> pdb=" O THR H 192 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'H' and resid 269 through 272 Processing sheet with id= BA, first strand: chain 'H' and resid 333 through 337 removed outlier: 3.617A pdb=" N ASP H 318 " --> pdb=" O LEU H 329 " (cutoff:3.500A) Processing sheet with id= BB, 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= BC, first strand: chain 'H' and resid 469 through 471 removed outlier: 3.693A pdb=" N SER H 422 " --> pdb=" O LEU H 435 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER H 437 " --> pdb=" O VAL H 420 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL H 420 " --> pdb=" O SER H 437 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'H' and resid 452 through 455 Processing sheet with id= BE, first strand: chain 'H' and resid 477 through 480 Processing sheet with id= BF, first strand: chain 'H' and resid 547 through 551 Processing sheet with id= BG, 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= BH, first strand: chain 'H' and resid 630 through 633 removed outlier: 8.622A pdb=" N TYR H 631 " --> pdb=" O VAL H 730 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU H 732 " --> pdb=" O TYR H 631 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N MET H 633 " --> pdb=" O GLU H 732 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP H 734 " --> pdb=" O MET H 633 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'H' and resid 666 through 676 removed outlier: 3.551A pdb=" N ILE H 645 " --> pdb=" O LYS H 682 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA H 621 " --> pdb=" O VAL H 646 " (cutoff:3.500A) Processing sheet with id= BJ, 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= BK, 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= BL, first strand: chain 'H' and resid 816 through 820 Processing sheet with id= BM, first strand: chain 'L' and resid 504 through 506 Processing sheet with id= BN, 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= BO, first strand: chain 'J' and resid 78 through 81 Processing sheet with id= BP, first strand: chain 'I' and resid 43 through 45 1938 hydrogen bonds defined for protein. 5313 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: 21.44 Time building geometry restraints manager: 19.93 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 - 23.96: 27836 23.96 - 47.92: 1568 47.92 - 71.88: 248 71.88 - 95.84: 147 95.84 - 119.81: 69 Dihedral angle restraints: 29868 sinusoidal: 12249 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 29865 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: 14223 2.81 - 3.51: 65638 3.51 - 4.20: 109536 4.20 - 4.90: 191646 Nonbonded interactions: 381079 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 381074 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 16.240 Check model and map are aligned: 0.720 Set scattering table: 0.420 Process input model: 125.970 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 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= 0.544 Angle : 1.151 12.681 66750 Z= 0.722 Chirality : 0.086 1.520 7837 Planarity : 0.008 0.157 8243 Dihedral : 17.103 119.806 18387 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.05 % Favored : 93.22 % Rotamer: Outliers : 2.98 % Allowed : 2.09 % Favored : 94.93 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP H 861 HIS 0.014 0.002 HIS E 45 PHE 0.062 0.003 PHE G 468 TYR 0.061 0.003 TYR F 138 ARG 0.009 0.001 ARG H 534 *********************** 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 : 5.024 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 REVERT: A 364 ASN cc_start: 0.7505 (t0) cc_final: 0.7225 (t160) REVERT: A 401 LEU cc_start: 0.7791 (mt) cc_final: 0.7514 (pp) REVERT: A 423 MET cc_start: 0.5733 (tpt) cc_final: 0.5448 (tpt) REVERT: A 496 MET cc_start: 0.8166 (ptm) cc_final: 0.7826 (ptm) REVERT: A 545 ASN cc_start: 0.8496 (m-40) cc_final: 0.8139 (m-40) REVERT: A 554 ILE cc_start: 0.8091 (tp) cc_final: 0.7794 (pt) REVERT: A 579 ASN cc_start: 0.8427 (m110) cc_final: 0.8172 (m110) REVERT: B 163 TRP cc_start: 0.6142 (m100) cc_final: 0.5854 (m-10) REVERT: B 180 PHE cc_start: 0.7803 (t80) cc_final: 0.7071 (t80) REVERT: B 221 ARG cc_start: 0.6846 (ttt90) cc_final: 0.6601 (ttm-80) REVERT: B 283 ASN cc_start: 0.8635 (m110) cc_final: 0.8222 (m-40) REVERT: C 88 LEU cc_start: 0.8408 (pp) cc_final: 0.8028 (tp) REVERT: C 188 MET cc_start: 0.8192 (mtm) cc_final: 0.7982 (mtm) REVERT: C 227 ASP cc_start: 0.6448 (t70) cc_final: 0.5921 (t0) REVERT: C 272 GLU cc_start: 0.7269 (tt0) cc_final: 0.6747 (mt-10) REVERT: D 113 ILE cc_start: 0.8135 (mt) cc_final: 0.7766 (tp) REVERT: D 187 MET cc_start: 0.7449 (tpt) cc_final: 0.7230 (mmm) REVERT: D 192 ASN cc_start: 0.7790 (m-40) cc_final: 0.7587 (m-40) REVERT: D 248 MET cc_start: 0.6759 (mmm) cc_final: 0.6199 (mmp) REVERT: D 255 MET cc_start: 0.7105 (mtt) cc_final: 0.6584 (mtp) REVERT: D 289 MET cc_start: 0.6276 (mpp) cc_final: 0.6057 (ttp) REVERT: E 453 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7512 (mppt) REVERT: E 685 MET cc_start: 0.7008 (ttm) cc_final: 0.6631 (ttp) REVERT: E 732 MET cc_start: 0.6716 (ppp) cc_final: 0.6477 (pp-130) REVERT: E 778 LYS cc_start: 0.8101 (mmtm) cc_final: 0.7489 (mppt) REVERT: E 884 THR cc_start: 0.7415 (OUTLIER) cc_final: 0.7132 (p) REVERT: E 904 SER cc_start: 0.7079 (t) cc_final: 0.6727 (m) REVERT: E 909 LYS cc_start: 0.6753 (mttm) cc_final: 0.6504 (tptp) REVERT: E 930 PHE cc_start: 0.7358 (t80) cc_final: 0.6752 (t80) REVERT: E 1050 ASP cc_start: 0.6347 (p0) cc_final: 0.5174 (t0) REVERT: F 147 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8838 (tt) REVERT: F 908 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.6757 (pttp) REVERT: F 1060 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.6573 (ttpp) REVERT: G 390 GLU cc_start: 0.8137 (pt0) cc_final: 0.7189 (tp30) REVERT: G 412 MET cc_start: 0.7842 (ttp) cc_final: 0.7464 (tmt) REVERT: G 611 SER cc_start: 0.8500 (t) cc_final: 0.8280 (t) REVERT: G 684 ASN cc_start: 0.7478 (t0) cc_final: 0.7275 (t0) REVERT: G 719 LYS cc_start: 0.5334 (OUTLIER) cc_final: 0.5007 (tptt) REVERT: G 721 GLN cc_start: 0.2486 (OUTLIER) cc_final: 0.0877 (mm-40) REVERT: H 699 ASN cc_start: 0.6683 (m110) cc_final: 0.6449 (p0) REVERT: H 933 ILE cc_start: 0.6434 (OUTLIER) cc_final: 0.5929 (tt) REVERT: L 129 ARG cc_start: 0.0392 (mtm-85) cc_final: 0.0049 (ptp90) REVERT: L 159 ARG cc_start: 0.3411 (mtm-85) cc_final: 0.2510 (pmt-80) REVERT: L 170 MET cc_start: 0.2150 (mmp) cc_final: 0.1925 (tpt) REVERT: L 234 MET cc_start: 0.1139 (tpt) cc_final: 0.0436 (tpt) REVERT: L 335 ARG cc_start: 0.2915 (ttp80) cc_final: 0.2639 (mtt-85) REVERT: L 466 CYS cc_start: 0.1441 (OUTLIER) cc_final: 0.0882 (m) REVERT: L 471 PHE cc_start: 0.4553 (OUTLIER) cc_final: 0.4114 (m-80) REVERT: L 637 ASN cc_start: 0.4067 (m-40) cc_final: 0.3567 (p0) REVERT: L 639 ARG cc_start: 0.0150 (tmt170) cc_final: -0.0693 (mmm160) REVERT: L 659 MET cc_start: 0.3160 (tpp) cc_final: 0.2833 (mpt) REVERT: M 17 MET cc_start: 0.4446 (tpp) cc_final: 0.4002 (tpt) REVERT: M 46 TYR cc_start: 0.7340 (m-10) cc_final: 0.7058 (m-10) outliers start: 148 outliers final: 44 residues processed: 1067 average time/residue: 1.4749 time to fit residues: 2012.2301 Evaluate side-chains 591 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 537 time to evaluate : 5.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 522 ASN Chi-restraints excluded: chain E residue 636 LEU Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 650 GLU Chi-restraints excluded: chain E residue 691 SER Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 721 ASN Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain E residue 834 LEU Chi-restraints excluded: chain E residue 881 ILE Chi-restraints excluded: chain E residue 884 THR Chi-restraints excluded: chain E residue 886 ASN Chi-restraints excluded: chain E residue 916 VAL Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1054 LEU Chi-restraints excluded: chain E residue 1056 PHE Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 402 ASN Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 621 ASN Chi-restraints excluded: chain F residue 641 LEU Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 907 ILE Chi-restraints excluded: chain F residue 908 LYS Chi-restraints excluded: chain F residue 953 LEU Chi-restraints excluded: chain F residue 956 ILE Chi-restraints excluded: chain F residue 1016 ILE Chi-restraints excluded: chain F residue 1053 HIS Chi-restraints excluded: chain F residue 1060 LYS Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 443 ASN Chi-restraints excluded: chain G residue 575 TYR Chi-restraints excluded: chain G residue 719 LYS Chi-restraints excluded: chain G residue 721 GLN Chi-restraints excluded: chain G residue 725 THR Chi-restraints excluded: chain H residue 91 ASN Chi-restraints excluded: chain H residue 445 ASN Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain H residue 933 ILE Chi-restraints excluded: chain L residue 466 CYS Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain L residue 471 PHE Chi-restraints excluded: chain L residue 549 GLU Chi-restraints excluded: chain M residue 112 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 501 optimal weight: 0.4980 chunk 450 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 153 optimal weight: 0.0370 chunk 303 optimal weight: 0.0470 chunk 240 optimal weight: 0.9980 chunk 465 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 283 optimal weight: 1.9990 chunk 346 optimal weight: 1.9990 chunk 539 optimal weight: 20.0000 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 364 ASN A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN D 185 GLN E 45 HIS ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN E 449 HIS ** E 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 719 GLN E 721 ASN E 839 HIS E 862 ASN E 876 HIS E 886 ASN E 928 GLN E 989 HIS F 67 GLN F 119 HIS F 130 ASN ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 427 GLN F 498 ASN ** F 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 228 HIS G 248 GLN G 443 ASN G 465 ASN G 517 ASN G 588 ASN G 644 ASN ** 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 ** H 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 ASN ** 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: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 49059 Z= 0.203 Angle : 0.710 13.676 66750 Z= 0.357 Chirality : 0.047 0.489 7837 Planarity : 0.005 0.087 8243 Dihedral : 12.103 100.095 8074 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.94 % Favored : 94.75 % Rotamer: Outliers : 3.62 % Allowed : 13.69 % Favored : 82.69 % 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: -0.59 (0.11), residues: 5929 helix: 0.58 (0.11), residues: 2020 sheet: 0.17 (0.14), residues: 1306 loop : -1.47 (0.12), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 175 HIS 0.012 0.001 HIS M 116 PHE 0.041 0.002 PHE G 720 TYR 0.021 0.001 TYR A 560 ARG 0.010 0.001 ARG E 59 *********************** 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 789 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 609 time to evaluate : 6.061 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: A 341 GLN cc_start: 0.6786 (mm110) cc_final: 0.6539 (mm-40) REVERT: A 376 LEU cc_start: 0.7819 (mt) cc_final: 0.7102 (tm) REVERT: A 400 VAL cc_start: 0.8222 (t) cc_final: 0.7922 (m) REVERT: A 401 LEU cc_start: 0.7708 (mt) cc_final: 0.7461 (pp) REVERT: A 518 ARG cc_start: 0.7619 (tpp-160) cc_final: 0.7416 (ttm110) REVERT: A 545 ASN cc_start: 0.8405 (m-40) cc_final: 0.8144 (m110) REVERT: A 552 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6221 (p90) REVERT: B 152 LEU cc_start: 0.7487 (mt) cc_final: 0.7240 (mp) REVERT: B 155 PHE cc_start: 0.7532 (m-80) cc_final: 0.7314 (m-80) REVERT: B 221 ARG cc_start: 0.6795 (ttt90) cc_final: 0.6594 (ttm-80) REVERT: B 283 ASN cc_start: 0.8687 (m110) cc_final: 0.8447 (m-40) REVERT: C 149 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: C 185 PHE cc_start: 0.7811 (t80) cc_final: 0.7441 (t80) REVERT: C 188 MET cc_start: 0.8143 (mtm) cc_final: 0.7910 (mtm) REVERT: C 272 GLU cc_start: 0.7169 (tt0) cc_final: 0.6623 (mt-10) REVERT: C 291 MET cc_start: 0.5422 (mmt) cc_final: 0.3796 (pmm) REVERT: D 113 ILE cc_start: 0.8163 (mt) cc_final: 0.7826 (tp) REVERT: D 185 GLN cc_start: 0.6900 (tp40) cc_final: 0.6698 (tp-100) REVERT: D 187 MET cc_start: 0.7420 (tpt) cc_final: 0.7117 (mmm) REVERT: D 247 GLN cc_start: 0.7189 (tm-30) cc_final: 0.6948 (tm-30) REVERT: D 248 MET cc_start: 0.6796 (mmm) cc_final: 0.6183 (mmp) REVERT: D 289 MET cc_start: 0.6532 (mpp) cc_final: 0.5758 (tmt) REVERT: E 559 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.5634 (tpp) REVERT: E 643 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7214 (mm) REVERT: E 671 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6371 (pmm) REVERT: E 685 MET cc_start: 0.7246 (ttm) cc_final: 0.6752 (ttp) REVERT: E 732 MET cc_start: 0.6724 (ppp) cc_final: 0.6421 (pp-130) REVERT: E 778 LYS cc_start: 0.8136 (mmtm) cc_final: 0.7497 (mppt) REVERT: E 855 HIS cc_start: 0.7223 (t-90) cc_final: 0.6680 (t-90) REVERT: E 981 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7076 (mpt) REVERT: E 1061 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7390 (tp) REVERT: F 626 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7884 (mt0) REVERT: F 665 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: F 735 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.6473 (mpp) REVERT: F 908 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.6679 (pttp) REVERT: F 918 ARG cc_start: 0.8272 (ttp-110) cc_final: 0.8071 (ttp-170) REVERT: F 1053 HIS cc_start: 0.8892 (OUTLIER) cc_final: 0.8565 (p90) REVERT: G 412 MET cc_start: 0.7970 (ttp) cc_final: 0.7554 (tmt) REVERT: G 576 ASP cc_start: 0.6990 (m-30) cc_final: 0.6776 (p0) REVERT: G 595 MET cc_start: 0.7702 (tmt) cc_final: 0.7279 (tmt) REVERT: G 622 ARG cc_start: 0.7408 (mpt180) cc_final: 0.7104 (mpt-90) REVERT: G 644 ASN cc_start: 0.6854 (OUTLIER) cc_final: 0.6584 (t0) REVERT: G 718 THR cc_start: 0.3675 (OUTLIER) cc_final: 0.3125 (m) REVERT: G 721 GLN cc_start: 0.2121 (OUTLIER) cc_final: 0.0773 (mm-40) REVERT: H 506 VAL cc_start: 0.9024 (m) cc_final: 0.8813 (t) REVERT: H 825 ASN cc_start: 0.6586 (OUTLIER) cc_final: 0.6317 (m-40) REVERT: H 867 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7538 (mmt90) REVERT: L 129 ARG cc_start: 0.0340 (mtm-85) cc_final: 0.0074 (ptp90) REVERT: L 159 ARG cc_start: 0.3689 (mtm-85) cc_final: 0.2630 (pmt170) REVERT: L 234 MET cc_start: 0.0925 (tpt) cc_final: 0.0581 (tpt) REVERT: L 335 ARG cc_start: 0.2719 (ttp80) cc_final: 0.2461 (mtm-85) REVERT: L 471 PHE cc_start: 0.4834 (OUTLIER) cc_final: 0.4369 (p90) REVERT: L 637 ASN cc_start: 0.4397 (m-40) cc_final: 0.3895 (p0) REVERT: L 639 ARG cc_start: -0.0334 (tmt170) cc_final: -0.1014 (mmm160) outliers start: 180 outliers final: 52 residues processed: 731 average time/residue: 1.3479 time to fit residues: 1276.4518 Evaluate side-chains 575 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 506 time to evaluate : 5.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 141 TYR Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 559 MET Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 671 MET Chi-restraints excluded: chain E residue 720 CYS Chi-restraints excluded: chain E residue 831 CYS Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 966 ILE Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 981 MET Chi-restraints excluded: chain E residue 1054 LEU Chi-restraints excluded: chain E residue 1061 LEU Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 531 ASN Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 626 GLN Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 665 GLU Chi-restraints excluded: chain F residue 735 MET Chi-restraints excluded: chain F residue 744 MET Chi-restraints excluded: chain F residue 908 LYS Chi-restraints excluded: chain F residue 1030 LEU Chi-restraints excluded: chain F residue 1053 HIS Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 295 SER Chi-restraints excluded: chain G residue 490 THR Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain G residue 644 ASN Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain G residue 721 GLN Chi-restraints excluded: chain G residue 724 LEU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 91 ASN Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 346 ASP Chi-restraints excluded: chain H residue 445 ASN Chi-restraints excluded: chain H residue 825 ASN Chi-restraints excluded: chain H residue 850 GLU Chi-restraints excluded: chain H residue 859 ASP Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain L residue 471 PHE Chi-restraints excluded: chain L residue 546 SER Chi-restraints excluded: chain L residue 670 VAL Chi-restraints excluded: chain M residue 103 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 299 optimal weight: 0.0670 chunk 167 optimal weight: 0.9990 chunk 448 optimal weight: 3.9990 chunk 367 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 540 optimal weight: 50.0000 chunk 583 optimal weight: 6.9990 chunk 481 optimal weight: 20.0000 chunk 535 optimal weight: 40.0000 chunk 184 optimal weight: 7.9990 chunk 433 optimal weight: 1.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN B 332 ASN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 646 ASN E 725 GLN E1000 HIS F 69 HIS F 144 ASN F 312 GLN F 313 ASN ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 622 GLN F 671 ASN F 679 GLN F 786 ASN F1018 GLN G 228 HIS ** G 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 607 GLN H 670 ASN L 364 ASN 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: 0.7241 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 49059 Z= 0.376 Angle : 0.741 14.373 66750 Z= 0.373 Chirality : 0.049 0.352 7837 Planarity : 0.005 0.062 8243 Dihedral : 9.429 86.741 7990 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.89 % Favored : 93.89 % Rotamer: Outliers : 4.45 % Allowed : 16.26 % Favored : 79.29 % 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: -0.53 (0.11), residues: 5929 helix: 0.74 (0.12), residues: 2028 sheet: 0.11 (0.14), residues: 1300 loop : -1.47 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 643 HIS 0.017 0.002 HIS M 116 PHE 0.034 0.002 PHE G 720 TYR 0.030 0.002 TYR G 44 ARG 0.013 0.001 ARG F 601 *********************** 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 766 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 545 time to evaluate : 5.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 VAL cc_start: 0.8250 (t) cc_final: 0.7986 (m) REVERT: A 401 LEU cc_start: 0.7670 (mt) cc_final: 0.7328 (pp) REVERT: A 423 MET cc_start: 0.6211 (tpt) cc_final: 0.5915 (tpt) REVERT: A 518 ARG cc_start: 0.7697 (tpp-160) cc_final: 0.7482 (ttm170) REVERT: A 545 ASN cc_start: 0.8496 (m-40) cc_final: 0.8229 (m110) REVERT: A 552 TYR cc_start: 0.7275 (OUTLIER) cc_final: 0.6213 (p90) REVERT: B 152 LEU cc_start: 0.7631 (mt) cc_final: 0.7386 (mt) REVERT: B 185 LEU cc_start: 0.8136 (tp) cc_final: 0.7875 (pp) REVERT: B 247 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7963 (mm) REVERT: B 353 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7595 (pp-130) REVERT: B 370 ILE cc_start: 0.4429 (mm) cc_final: 0.4017 (pt) REVERT: C 188 MET cc_start: 0.8205 (mtm) cc_final: 0.7994 (mtm) REVERT: C 272 GLU cc_start: 0.7272 (tt0) cc_final: 0.6771 (mt-10) REVERT: C 291 MET cc_start: 0.5541 (mmt) cc_final: 0.3999 (pmm) REVERT: D 113 ILE cc_start: 0.8204 (mt) cc_final: 0.7859 (tp) REVERT: D 187 MET cc_start: 0.7391 (tpt) cc_final: 0.7105 (mmm) REVERT: D 247 GLN cc_start: 0.7084 (tm-30) cc_final: 0.6868 (tm-30) REVERT: D 248 MET cc_start: 0.6781 (mmm) cc_final: 0.6195 (mmp) REVERT: D 289 MET cc_start: 0.6417 (mpp) cc_final: 0.5907 (tmm) REVERT: E 523 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8482 (t) REVERT: E 671 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6444 (pmm) REVERT: E 685 MET cc_start: 0.7583 (ttm) cc_final: 0.7206 (ttp) REVERT: E 715 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8377 (mm) REVERT: E 732 MET cc_start: 0.6852 (ppp) cc_final: 0.6470 (pp-130) REVERT: E 778 LYS cc_start: 0.8297 (mmtm) cc_final: 0.7749 (mppt) REVERT: E 899 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7711 (t0) REVERT: F 216 LYS cc_start: 0.7755 (ptmt) cc_final: 0.7507 (pttm) REVERT: F 335 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7348 (ptp-170) REVERT: F 562 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7188 (mmt) REVERT: F 665 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7175 (tt0) REVERT: F 735 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8052 (mtt) REVERT: F 846 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7841 (ttp) REVERT: F 908 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6488 (pttp) REVERT: F 1037 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7673 (t0) REVERT: F 1039 SER cc_start: 0.8461 (t) cc_final: 0.8155 (m) REVERT: F 1053 HIS cc_start: 0.9053 (OUTLIER) cc_final: 0.8667 (p90) REVERT: G 281 PHE cc_start: 0.7401 (p90) cc_final: 0.6667 (p90) REVERT: G 622 ARG cc_start: 0.7458 (mpt180) cc_final: 0.7211 (mpt-90) REVERT: G 718 THR cc_start: 0.3694 (OUTLIER) cc_final: 0.3270 (m) REVERT: G 721 GLN cc_start: 0.2372 (OUTLIER) cc_final: 0.0628 (mm-40) REVERT: G 725 THR cc_start: 0.4741 (OUTLIER) cc_final: 0.4533 (m) REVERT: H 225 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8441 (mt) REVERT: H 515 GLU cc_start: 0.7431 (tp30) cc_final: 0.7154 (tp30) REVERT: H 534 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7664 (mtm180) REVERT: H 672 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6982 (tp30) REVERT: H 685 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8858 (mm) REVERT: L 129 ARG cc_start: 0.0378 (mtm-85) cc_final: -0.0029 (mmt180) REVERT: L 159 ARG cc_start: 0.3683 (mtm-85) cc_final: 0.2589 (pmt170) REVERT: L 335 ARG cc_start: 0.2700 (ttp80) cc_final: 0.2462 (mtm-85) REVERT: L 435 ARG cc_start: 0.2820 (tpt170) cc_final: 0.2268 (mmm160) REVERT: L 471 PHE cc_start: 0.4425 (OUTLIER) cc_final: 0.4004 (p90) REVERT: L 580 PHE cc_start: 0.7814 (m-10) cc_final: 0.7594 (m-10) REVERT: L 637 ASN cc_start: 0.4439 (m-40) cc_final: 0.3779 (p0) outliers start: 221 outliers final: 86 residues processed: 709 average time/residue: 1.3465 time to fit residues: 1242.7433 Evaluate side-chains 574 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 465 time to evaluate : 5.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 TYR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 523 SER Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 571 THR Chi-restraints excluded: chain E residue 671 MET Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain E residue 720 CYS Chi-restraints excluded: chain E residue 782 VAL Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 899 ASN Chi-restraints excluded: chain E residue 966 ILE Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain E residue 981 MET Chi-restraints excluded: chain E residue 998 MET Chi-restraints excluded: chain E residue 1054 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 260 LYS Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 335 ARG Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 531 ASN Chi-restraints excluded: chain F residue 562 MET Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 665 GLU Chi-restraints excluded: chain F residue 712 THR Chi-restraints excluded: chain F residue 735 MET Chi-restraints excluded: chain F residue 744 MET Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 806 THR Chi-restraints excluded: chain F residue 842 LYS Chi-restraints excluded: chain F residue 846 MET Chi-restraints excluded: chain F residue 872 VAL Chi-restraints excluded: chain F residue 888 VAL Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 908 LYS Chi-restraints excluded: chain F residue 941 SER Chi-restraints excluded: chain F residue 1030 LEU Chi-restraints excluded: chain F residue 1037 ASP Chi-restraints excluded: chain F residue 1053 HIS Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 126 LYS Chi-restraints excluded: chain G residue 295 SER Chi-restraints excluded: chain G residue 490 THR Chi-restraints excluded: chain G residue 573 VAL Chi-restraints excluded: chain G residue 592 GLU Chi-restraints excluded: chain G residue 669 VAL Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain G residue 721 GLN Chi-restraints excluded: chain G residue 725 THR Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain H residue 307 ILE Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 534 ARG Chi-restraints excluded: chain H residue 562 THR Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain H residue 672 GLU Chi-restraints excluded: chain H residue 685 ILE Chi-restraints excluded: chain H residue 708 THR Chi-restraints excluded: chain H residue 859 ASP Chi-restraints excluded: chain H residue 933 ILE Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain L residue 471 PHE Chi-restraints excluded: chain L residue 475 ASN Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain L residue 579 VAL Chi-restraints excluded: chain L residue 670 VAL Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain M residue 44 HIS Chi-restraints excluded: chain M residue 103 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 533 optimal weight: 20.0000 chunk 406 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 257 optimal weight: 0.9980 chunk 362 optimal weight: 0.5980 chunk 542 optimal weight: 40.0000 chunk 574 optimal weight: 0.2980 chunk 283 optimal weight: 0.5980 chunk 513 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 332 ASN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN G 228 HIS G 290 ASN G 588 ASN H 182 ASN H 233 GLN H 469 GLN H 607 GLN H 670 ASN ** H 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 152 HIS L 426 HIS L 475 ASN ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3269 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= 0.179 Angle : 0.634 14.704 66750 Z= 0.318 Chirality : 0.045 0.377 7837 Planarity : 0.004 0.050 8243 Dihedral : 8.005 80.535 7984 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.26 % Favored : 94.55 % Rotamer: Outliers : 3.72 % Allowed : 18.88 % Favored : 77.40 % 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: -0.38 (0.11), residues: 5929 helix: 0.91 (0.12), residues: 2042 sheet: 0.17 (0.14), residues: 1275 loop : -1.41 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 98 HIS 0.012 0.001 HIS M 44 PHE 0.031 0.001 PHE G 720 TYR 0.023 0.001 TYR M 46 ARG 0.007 0.000 ARG M 115 *********************** 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 726 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 541 time to evaluate : 5.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 VAL cc_start: 0.8242 (t) cc_final: 0.7981 (m) REVERT: A 401 LEU cc_start: 0.7660 (mt) cc_final: 0.7335 (pp) REVERT: A 419 ASP cc_start: 0.7503 (t0) cc_final: 0.7237 (m-30) REVERT: A 436 ASN cc_start: 0.6253 (m110) cc_final: 0.5897 (m110) REVERT: A 545 ASN cc_start: 0.8461 (m-40) cc_final: 0.8181 (m110) REVERT: A 552 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6204 (p90) REVERT: A 554 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7940 (pt) REVERT: B 152 LEU cc_start: 0.7647 (mt) cc_final: 0.7442 (mt) REVERT: B 155 PHE cc_start: 0.7616 (m-80) cc_final: 0.7269 (m-80) REVERT: B 180 PHE cc_start: 0.7693 (t80) cc_final: 0.7208 (t80) REVERT: B 185 LEU cc_start: 0.8104 (tp) cc_final: 0.7790 (pp) REVERT: B 247 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7917 (mm) REVERT: B 370 ILE cc_start: 0.4454 (mm) cc_final: 0.4050 (pt) REVERT: C 42 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.7282 (t80) REVERT: C 53 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6923 (mm-40) REVERT: C 66 LEU cc_start: 0.8311 (mt) cc_final: 0.8096 (mt) REVERT: C 185 PHE cc_start: 0.7890 (t80) cc_final: 0.7511 (t80) REVERT: C 272 GLU cc_start: 0.7239 (tt0) cc_final: 0.6693 (mt-10) REVERT: C 291 MET cc_start: 0.5721 (mmt) cc_final: 0.4148 (pmm) REVERT: D 113 ILE cc_start: 0.8246 (mt) cc_final: 0.7963 (tp) REVERT: D 187 MET cc_start: 0.7370 (tpt) cc_final: 0.7034 (mmm) REVERT: D 247 GLN cc_start: 0.7051 (tm-30) cc_final: 0.6745 (tm-30) REVERT: D 248 MET cc_start: 0.6755 (mmm) cc_final: 0.5924 (mpm) REVERT: D 289 MET cc_start: 0.6504 (mpp) cc_final: 0.5666 (tmm) REVERT: E 441 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7015 (tt0) REVERT: E 671 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6603 (pmm) REVERT: E 685 MET cc_start: 0.7578 (ttm) cc_final: 0.7322 (ttp) REVERT: E 732 MET cc_start: 0.6883 (ppp) cc_final: 0.6636 (pp-130) REVERT: E 778 LYS cc_start: 0.8284 (mmtm) cc_final: 0.7745 (mppt) REVERT: E 780 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: E 899 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7493 (m110) REVERT: E 998 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8398 (mmm) REVERT: E 1021 GLN cc_start: 0.7330 (mp10) cc_final: 0.7115 (mp-120) REVERT: F 200 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7663 (ttp-170) REVERT: F 216 LYS cc_start: 0.7808 (ptmt) cc_final: 0.7529 (pttm) REVERT: F 419 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8405 (pp) REVERT: F 665 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: F 735 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8062 (mtt) REVERT: F 908 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6496 (pttp) REVERT: F 951 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6892 (mmm160) REVERT: F 1039 SER cc_start: 0.8415 (t) cc_final: 0.8195 (m) REVERT: G 622 ARG cc_start: 0.7389 (mpt180) cc_final: 0.7116 (mpt-90) REVERT: G 718 THR cc_start: 0.3533 (OUTLIER) cc_final: 0.3112 (m) REVERT: G 721 GLN cc_start: 0.2460 (OUTLIER) cc_final: 0.0743 (mm-40) REVERT: H 181 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8555 (mmt) REVERT: H 225 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8331 (mt) REVERT: H 493 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7507 (pt0) REVERT: H 612 ASP cc_start: 0.5955 (OUTLIER) cc_final: 0.5752 (m-30) REVERT: H 639 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8533 (tp) REVERT: L 129 ARG cc_start: 0.0403 (mtm-85) cc_final: 0.0023 (mmt180) REVERT: L 335 ARG cc_start: 0.2658 (ttp80) cc_final: 0.2442 (mtm-85) REVERT: L 390 THR cc_start: 0.6789 (m) cc_final: 0.6305 (t) REVERT: L 435 ARG cc_start: 0.2867 (tpt170) cc_final: 0.1908 (mpp-170) REVERT: L 471 PHE cc_start: 0.4317 (OUTLIER) cc_final: 0.3854 (p90) REVERT: L 571 PHE cc_start: 0.4827 (OUTLIER) cc_final: 0.4626 (m-80) REVERT: L 637 ASN cc_start: 0.4411 (m-40) cc_final: 0.3704 (p0) REVERT: M 73 LEU cc_start: 0.8122 (mm) cc_final: 0.7885 (tp) REVERT: M 101 ARG cc_start: 0.7981 (tpp-160) cc_final: 0.7761 (tpp-160) outliers start: 185 outliers final: 76 residues processed: 671 average time/residue: 1.3473 time to fit residues: 1174.7424 Evaluate side-chains 590 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 489 time to evaluate : 5.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain C residue 42 TYR Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 TYR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 441 GLU Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 571 THR Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 671 MET Chi-restraints excluded: chain E residue 720 CYS Chi-restraints excluded: chain E residue 780 GLN Chi-restraints excluded: chain E residue 832 SER Chi-restraints excluded: chain E residue 899 ASN Chi-restraints excluded: chain E residue 966 ILE Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 998 MET Chi-restraints excluded: chain E residue 1062 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 200 ARG Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 463 ASP Chi-restraints excluded: chain F residue 531 ASN Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 665 GLU Chi-restraints excluded: chain F residue 712 THR Chi-restraints excluded: chain F residue 735 MET Chi-restraints excluded: chain F residue 744 MET Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 806 THR Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 908 LYS Chi-restraints excluded: chain F residue 951 ARG Chi-restraints excluded: chain F residue 977 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 295 SER Chi-restraints excluded: chain G residue 490 THR Chi-restraints excluded: chain G residue 669 VAL Chi-restraints excluded: chain G residue 674 THR Chi-restraints excluded: chain G residue 683 ARG Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain G residue 721 GLN Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 346 ASP Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 493 GLN Chi-restraints excluded: chain H residue 612 ASP Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain H residue 665 MET Chi-restraints excluded: chain H residue 708 THR Chi-restraints excluded: chain H residue 859 ASP Chi-restraints excluded: chain H residue 924 ILE Chi-restraints excluded: chain H residue 933 ILE Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 471 PHE Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain L residue 571 PHE Chi-restraints excluded: chain L residue 579 VAL Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain M residue 103 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 478 optimal weight: 30.0000 chunk 325 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 427 optimal weight: 0.6980 chunk 236 optimal weight: 0.8980 chunk 489 optimal weight: 5.9990 chunk 396 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 293 optimal weight: 0.9980 chunk 515 optimal weight: 0.6980 chunk 144 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** D 185 GLN E 889 HIS F 130 ASN F 146 GLN ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN F 648 HIS F1018 GLN G 74 ASN G 228 HIS G 644 ASN H 517 ASN H 607 GLN H 670 ASN ** H 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 GLN ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 49059 Z= 0.183 Angle : 0.622 15.077 66750 Z= 0.311 Chirality : 0.045 0.757 7837 Planarity : 0.004 0.050 8243 Dihedral : 7.241 76.434 7978 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.50 % Favored : 94.30 % Rotamer: Outliers : 4.03 % Allowed : 19.77 % Favored : 76.21 % 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: -0.33 (0.11), residues: 5929 helix: 1.01 (0.12), residues: 2061 sheet: 0.18 (0.14), residues: 1283 loop : -1.45 (0.12), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 98 HIS 0.005 0.001 HIS L 426 PHE 0.042 0.001 PHE A 358 TYR 0.023 0.001 TYR E 550 ARG 0.011 0.000 ARG A 467 *********************** 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 726 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 526 time to evaluate : 6.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 GLU cc_start: 0.7435 (pp20) cc_final: 0.6703 (pm20) REVERT: A 400 VAL cc_start: 0.8219 (t) cc_final: 0.7969 (m) REVERT: A 401 LEU cc_start: 0.7593 (mt) cc_final: 0.7246 (pp) REVERT: A 419 ASP cc_start: 0.7414 (t0) cc_final: 0.7160 (m-30) REVERT: A 423 MET cc_start: 0.5505 (tpt) cc_final: 0.5198 (tpt) REVERT: A 425 MET cc_start: 0.7172 (mmp) cc_final: 0.6815 (tpt) REVERT: A 436 ASN cc_start: 0.6196 (m110) cc_final: 0.5805 (m110) REVERT: A 518 ARG cc_start: 0.7697 (tpp-160) cc_final: 0.7398 (mmt-90) REVERT: A 533 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8066 (mp) REVERT: A 545 ASN cc_start: 0.8445 (m-40) cc_final: 0.8166 (m110) REVERT: A 552 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.6333 (p90) REVERT: A 554 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7952 (pt) REVERT: B 180 PHE cc_start: 0.7830 (t80) cc_final: 0.7340 (t80) REVERT: B 185 LEU cc_start: 0.7967 (tp) cc_final: 0.7671 (pp) REVERT: B 247 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7919 (mm) REVERT: B 353 MET cc_start: 0.7811 (pp-130) cc_final: 0.7524 (pp-130) REVERT: C 42 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.7273 (t80) REVERT: C 185 PHE cc_start: 0.7903 (t80) cc_final: 0.7515 (t80) REVERT: C 272 GLU cc_start: 0.7237 (tt0) cc_final: 0.6942 (mt-10) REVERT: C 291 MET cc_start: 0.5699 (mmt) cc_final: 0.4153 (pmm) REVERT: D 113 ILE cc_start: 0.8234 (mt) cc_final: 0.7956 (tp) REVERT: D 187 MET cc_start: 0.7262 (tpt) cc_final: 0.6956 (mmm) REVERT: D 194 MET cc_start: 0.7224 (mtt) cc_final: 0.6937 (mtt) REVERT: D 247 GLN cc_start: 0.6952 (tm-30) cc_final: 0.6692 (tm-30) REVERT: D 248 MET cc_start: 0.6697 (mmm) cc_final: 0.5872 (mpm) REVERT: D 289 MET cc_start: 0.6498 (mpp) cc_final: 0.5753 (tmt) REVERT: E 277 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7461 (tppt) REVERT: E 559 MET cc_start: 0.5921 (tpp) cc_final: 0.5512 (ttt) REVERT: E 585 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8601 (tp) REVERT: E 671 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6669 (pmm) REVERT: E 685 MET cc_start: 0.7579 (ttm) cc_final: 0.7245 (ttp) REVERT: E 732 MET cc_start: 0.7019 (ppp) cc_final: 0.6762 (pp-130) REVERT: E 775 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8800 (p) REVERT: E 778 LYS cc_start: 0.8283 (mmtm) cc_final: 0.7725 (mppt) REVERT: E 780 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7263 (tm-30) REVERT: E 899 ASN cc_start: 0.7603 (OUTLIER) cc_final: 0.7356 (m110) REVERT: E 1021 GLN cc_start: 0.7276 (mp10) cc_final: 0.6835 (mp10) REVERT: E 1062 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7291 (mp) REVERT: F 200 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7685 (ttp-170) REVERT: F 216 LYS cc_start: 0.7811 (ptmt) cc_final: 0.7500 (pttm) REVERT: F 517 MET cc_start: 0.8366 (ttm) cc_final: 0.8026 (mtm) REVERT: F 612 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8072 (m-40) REVERT: F 665 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7263 (tt0) REVERT: F 735 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7977 (mtt) REVERT: F 908 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6532 (pttp) REVERT: F 951 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6917 (mmm160) REVERT: F 980 LYS cc_start: 0.8373 (ptmm) cc_final: 0.8028 (ptmm) REVERT: F 1039 SER cc_start: 0.8424 (t) cc_final: 0.8214 (m) REVERT: G 622 ARG cc_start: 0.7386 (mpt180) cc_final: 0.7136 (mpt-90) REVERT: G 718 THR cc_start: 0.3852 (OUTLIER) cc_final: 0.3428 (m) REVERT: G 721 GLN cc_start: 0.2395 (OUTLIER) cc_final: 0.0674 (mm-40) REVERT: H 225 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8271 (mt) REVERT: H 493 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7510 (pt0) REVERT: H 534 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7619 (mtm180) REVERT: H 612 ASP cc_start: 0.5998 (OUTLIER) cc_final: 0.5581 (m-30) REVERT: H 639 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8555 (tp) REVERT: L 100 TYR cc_start: 0.2187 (t80) cc_final: 0.1821 (t80) REVERT: L 129 ARG cc_start: 0.0397 (mtm-85) cc_final: 0.0134 (ptp90) REVERT: L 390 THR cc_start: 0.6792 (m) cc_final: 0.6558 (m) REVERT: L 435 ARG cc_start: 0.2791 (tpt170) cc_final: 0.1641 (mpp-170) REVERT: L 471 PHE cc_start: 0.4455 (OUTLIER) cc_final: 0.4030 (p90) REVERT: L 490 ASP cc_start: 0.5153 (OUTLIER) cc_final: 0.4694 (t0) REVERT: L 625 ARG cc_start: 0.4631 (mmm-85) cc_final: 0.4236 (mmp80) REVERT: L 637 ASN cc_start: 0.4432 (m-40) cc_final: 0.3734 (p0) REVERT: L 659 MET cc_start: 0.2773 (mmm) cc_final: 0.2230 (mmm) REVERT: L 663 MET cc_start: 0.2282 (ptt) cc_final: 0.1859 (ptt) REVERT: M 77 MET cc_start: 0.6889 (ttt) cc_final: 0.6332 (pp-130) outliers start: 200 outliers final: 75 residues processed: 676 average time/residue: 1.3194 time to fit residues: 1158.0081 Evaluate side-chains 588 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 486 time to evaluate : 5.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 42 TYR Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 TYR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 571 THR Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 671 MET Chi-restraints excluded: chain E residue 775 VAL Chi-restraints excluded: chain E residue 780 GLN Chi-restraints excluded: chain E residue 832 SER Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 899 ASN Chi-restraints excluded: chain E residue 965 LYS Chi-restraints excluded: chain E residue 966 ILE Chi-restraints excluded: chain E residue 1062 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 200 ARG Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 466 THR Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 612 ASN Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 653 THR Chi-restraints excluded: chain F residue 665 GLU Chi-restraints excluded: chain F residue 712 THR Chi-restraints excluded: chain F residue 735 MET Chi-restraints excluded: chain F residue 744 MET Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 806 THR Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 908 LYS Chi-restraints excluded: chain F residue 919 ASP Chi-restraints excluded: chain F residue 951 ARG Chi-restraints excluded: chain F residue 977 LEU Chi-restraints excluded: chain F residue 986 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 295 SER Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain G residue 490 THR Chi-restraints excluded: chain G residue 669 VAL Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain G residue 721 GLN Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 346 ASP Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 493 GLN Chi-restraints excluded: chain H residue 534 ARG Chi-restraints excluded: chain H residue 537 ASN Chi-restraints excluded: chain H residue 556 GLU Chi-restraints excluded: chain H residue 562 THR Chi-restraints excluded: chain H residue 612 ASP Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain H residue 665 MET Chi-restraints excluded: chain H residue 671 LEU Chi-restraints excluded: chain H residue 859 ASP Chi-restraints excluded: chain H residue 924 ILE Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 287 THR Chi-restraints excluded: chain L residue 471 PHE Chi-restraints excluded: chain L residue 490 ASP Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain L residue 579 VAL Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain M residue 44 HIS Chi-restraints excluded: chain M residue 103 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 193 optimal weight: 0.8980 chunk 517 optimal weight: 0.0270 chunk 113 optimal weight: 0.9980 chunk 337 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 574 optimal weight: 5.9990 chunk 477 optimal weight: 40.0000 chunk 266 optimal weight: 0.0270 chunk 47 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 chunk 301 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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** D 151 GLN D 185 GLN F 128 GLN F 146 GLN ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN H 607 GLN H 670 ASN H 835 GLN ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 49059 Z= 0.167 Angle : 0.606 14.557 66750 Z= 0.303 Chirality : 0.044 0.577 7837 Planarity : 0.004 0.052 8243 Dihedral : 6.780 72.881 7978 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.38 % Rotamer: Outliers : 3.66 % Allowed : 21.01 % Favored : 75.32 % 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: -0.22 (0.11), residues: 5929 helix: 1.15 (0.12), residues: 2068 sheet: 0.23 (0.14), residues: 1279 loop : -1.43 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 98 HIS 0.026 0.001 HIS M 44 PHE 0.029 0.001 PHE G 720 TYR 0.021 0.001 TYR G 538 ARG 0.011 0.000 ARG A 467 *********************** 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 705 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 523 time to evaluate : 5.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 VAL cc_start: 0.8143 (t) cc_final: 0.7883 (m) REVERT: A 401 LEU cc_start: 0.7548 (mt) cc_final: 0.7193 (pp) REVERT: A 419 ASP cc_start: 0.7394 (t0) cc_final: 0.7169 (m-30) REVERT: A 436 ASN cc_start: 0.6196 (m110) cc_final: 0.5738 (m110) REVERT: A 518 ARG cc_start: 0.7720 (tpp-160) cc_final: 0.7458 (mmt-90) REVERT: A 519 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6187 (p90) REVERT: A 533 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.7973 (mp) REVERT: A 541 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7284 (pt) REVERT: A 545 ASN cc_start: 0.8429 (m-40) cc_final: 0.8174 (m110) REVERT: A 552 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.6879 (p90) REVERT: A 554 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7967 (pt) REVERT: B 180 PHE cc_start: 0.7798 (t80) cc_final: 0.7336 (t80) REVERT: B 185 LEU cc_start: 0.7965 (tp) cc_final: 0.7690 (pp) REVERT: B 247 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7908 (mt) REVERT: B 341 ASN cc_start: 0.7613 (t0) cc_final: 0.7306 (t0) REVERT: C 42 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.7440 (t80) REVERT: C 185 PHE cc_start: 0.7877 (t80) cc_final: 0.7508 (t80) REVERT: C 272 GLU cc_start: 0.7251 (tt0) cc_final: 0.7000 (mt-10) REVERT: C 291 MET cc_start: 0.5863 (mmt) cc_final: 0.4291 (pmm) REVERT: D 113 ILE cc_start: 0.8292 (mt) cc_final: 0.8026 (tp) REVERT: D 151 GLN cc_start: 0.5429 (tt0) cc_final: 0.4198 (tt0) REVERT: D 187 MET cc_start: 0.7147 (tpt) cc_final: 0.6869 (mmm) REVERT: D 194 MET cc_start: 0.7252 (mtt) cc_final: 0.6974 (mtt) REVERT: D 205 SER cc_start: 0.8143 (t) cc_final: 0.7222 (p) REVERT: D 247 GLN cc_start: 0.6939 (tm-30) cc_final: 0.6678 (tm-30) REVERT: D 248 MET cc_start: 0.6728 (mmm) cc_final: 0.5875 (mpm) REVERT: D 289 MET cc_start: 0.6392 (mpp) cc_final: 0.5592 (tmt) REVERT: E 468 GLU cc_start: 0.5621 (OUTLIER) cc_final: 0.5168 (pt0) REVERT: E 469 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7127 (p0) REVERT: E 559 MET cc_start: 0.5959 (tpp) cc_final: 0.5646 (ttt) REVERT: E 585 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8400 (tp) REVERT: E 671 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6652 (pmm) REVERT: E 685 MET cc_start: 0.7496 (ttm) cc_final: 0.7279 (ttp) REVERT: E 732 MET cc_start: 0.7142 (ppp) cc_final: 0.6758 (pp-130) REVERT: E 775 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8771 (p) REVERT: E 778 LYS cc_start: 0.8298 (mmtm) cc_final: 0.7723 (mppt) REVERT: E 780 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: E 899 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.7069 (t0) REVERT: E 1021 GLN cc_start: 0.7278 (mp10) cc_final: 0.6875 (mp10) REVERT: E 1062 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7300 (mp) REVERT: F 200 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7672 (ttp-170) REVERT: F 216 LYS cc_start: 0.7859 (ptmt) cc_final: 0.7531 (pttm) REVERT: F 517 MET cc_start: 0.8338 (ttm) cc_final: 0.8012 (mtm) REVERT: F 612 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8064 (m-40) REVERT: F 665 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: F 735 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7978 (mtt) REVERT: F 908 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6524 (pttp) REVERT: F 951 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6903 (mmm160) REVERT: F 1039 SER cc_start: 0.8424 (t) cc_final: 0.8221 (m) REVERT: G 440 GLU cc_start: 0.7330 (tm-30) cc_final: 0.6846 (tm-30) REVERT: G 622 ARG cc_start: 0.7373 (mpt180) cc_final: 0.7172 (mpt-90) REVERT: G 718 THR cc_start: 0.3779 (OUTLIER) cc_final: 0.3330 (m) REVERT: G 721 GLN cc_start: 0.2177 (OUTLIER) cc_final: 0.0505 (mm-40) REVERT: H 493 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7444 (pt0) REVERT: H 612 ASP cc_start: 0.5907 (OUTLIER) cc_final: 0.5520 (m-30) REVERT: H 639 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8603 (tp) REVERT: H 685 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8785 (mm) REVERT: L 129 ARG cc_start: 0.0417 (mtm-85) cc_final: 0.0142 (ptp90) REVERT: L 227 CYS cc_start: 0.5305 (m) cc_final: 0.4701 (m) REVERT: L 390 THR cc_start: 0.6792 (m) cc_final: 0.6307 (t) REVERT: L 435 ARG cc_start: 0.2698 (tpt170) cc_final: 0.1536 (mpp-170) REVERT: L 471 PHE cc_start: 0.4636 (OUTLIER) cc_final: 0.4175 (p90) REVERT: L 625 ARG cc_start: 0.4730 (mmm-85) cc_final: 0.4339 (mmp80) REVERT: L 637 ASN cc_start: 0.4586 (m-40) cc_final: 0.3854 (p0) REVERT: L 659 MET cc_start: 0.2798 (mmm) cc_final: 0.2159 (mmm) REVERT: L 663 MET cc_start: 0.2413 (ptt) cc_final: 0.2040 (ptt) REVERT: M 77 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6459 (pp-130) outliers start: 182 outliers final: 74 residues processed: 650 average time/residue: 1.3443 time to fit residues: 1134.3034 Evaluate side-chains 594 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 491 time to evaluate : 5.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 42 TYR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 571 THR Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 671 MET Chi-restraints excluded: chain E residue 720 CYS Chi-restraints excluded: chain E residue 775 VAL Chi-restraints excluded: chain E residue 780 GLN Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 899 ASN Chi-restraints excluded: chain E residue 966 ILE Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 1062 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 200 ARG Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain F residue 466 THR Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 612 ASN Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 653 THR Chi-restraints excluded: chain F residue 665 GLU Chi-restraints excluded: chain F residue 712 THR Chi-restraints excluded: chain F residue 735 MET Chi-restraints excluded: chain F residue 744 MET Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 908 LYS Chi-restraints excluded: chain F residue 919 ASP Chi-restraints excluded: chain F residue 951 ARG Chi-restraints excluded: chain F residue 986 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 295 SER Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 669 VAL Chi-restraints excluded: chain G residue 674 THR Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain G residue 721 GLN Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 445 ASN Chi-restraints excluded: chain H residue 493 GLN Chi-restraints excluded: chain H residue 537 ASN Chi-restraints excluded: chain H residue 556 GLU Chi-restraints excluded: chain H residue 612 ASP Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain H residue 665 MET Chi-restraints excluded: chain H residue 685 ILE Chi-restraints excluded: chain H residue 708 THR Chi-restraints excluded: chain H residue 859 ASP Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 287 THR Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 471 PHE Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain L residue 579 VAL Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain M residue 77 MET Chi-restraints excluded: chain M residue 103 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 554 optimal weight: 0.0070 chunk 64 optimal weight: 0.1980 chunk 327 optimal weight: 0.8980 chunk 419 optimal weight: 5.9990 chunk 325 optimal weight: 2.9990 chunk 483 optimal weight: 30.0000 chunk 320 optimal weight: 1.9990 chunk 572 optimal weight: 40.0000 chunk 358 optimal weight: 4.9990 chunk 349 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN F 146 GLN ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 290 ASN G 516 GLN 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: 0.7220 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 49059 Z= 0.229 Angle : 0.635 15.435 66750 Z= 0.317 Chirality : 0.045 0.462 7837 Planarity : 0.004 0.077 8243 Dihedral : 6.688 71.815 7978 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.65 % Favored : 94.18 % Rotamer: Outliers : 3.70 % Allowed : 21.64 % Favored : 74.66 % 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: -0.17 (0.11), residues: 5929 helix: 1.23 (0.12), residues: 2060 sheet: 0.22 (0.14), residues: 1282 loop : -1.41 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 98 HIS 0.006 0.001 HIS M 44 PHE 0.046 0.002 PHE A 358 TYR 0.026 0.001 TYR A 560 ARG 0.012 0.000 ARG A 467 *********************** 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 702 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 518 time to evaluate : 5.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 VAL cc_start: 0.8180 (t) cc_final: 0.7939 (m) REVERT: A 401 LEU cc_start: 0.7540 (mt) cc_final: 0.7173 (pp) REVERT: A 419 ASP cc_start: 0.7429 (t0) cc_final: 0.7181 (m-30) REVERT: A 425 MET cc_start: 0.7198 (tpp) cc_final: 0.6902 (tpt) REVERT: A 436 ASN cc_start: 0.6274 (m110) cc_final: 0.5833 (m110) REVERT: A 518 ARG cc_start: 0.7709 (tpp-160) cc_final: 0.7412 (mmt-90) REVERT: A 519 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.6194 (p90) REVERT: A 533 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7989 (mp) REVERT: A 541 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7314 (pt) REVERT: A 545 ASN cc_start: 0.8399 (m-40) cc_final: 0.8136 (m110) REVERT: B 180 PHE cc_start: 0.7801 (t80) cc_final: 0.7339 (t80) REVERT: B 185 LEU cc_start: 0.7985 (tp) cc_final: 0.7707 (pp) REVERT: B 247 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7945 (mt) REVERT: C 272 GLU cc_start: 0.7275 (tt0) cc_final: 0.7017 (mt-10) REVERT: C 275 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6799 (ppp) REVERT: C 291 MET cc_start: 0.5860 (mmt) cc_final: 0.4300 (pmm) REVERT: D 113 ILE cc_start: 0.8306 (mt) cc_final: 0.8045 (tp) REVERT: D 187 MET cc_start: 0.6986 (tpt) cc_final: 0.6730 (mmm) REVERT: D 194 MET cc_start: 0.7287 (mtt) cc_final: 0.7016 (mtt) REVERT: D 205 SER cc_start: 0.8185 (t) cc_final: 0.7293 (p) REVERT: D 247 GLN cc_start: 0.6947 (tm-30) cc_final: 0.6677 (tm-30) REVERT: D 248 MET cc_start: 0.6732 (mmm) cc_final: 0.5898 (mpm) REVERT: D 289 MET cc_start: 0.6388 (mpp) cc_final: 0.5578 (tmt) REVERT: E 585 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8752 (tp) REVERT: E 671 MET cc_start: 0.7203 (pmm) cc_final: 0.6687 (pmm) REVERT: E 685 MET cc_start: 0.7581 (ttm) cc_final: 0.7299 (ttp) REVERT: E 732 MET cc_start: 0.7150 (ppp) cc_final: 0.6803 (pp-130) REVERT: E 775 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8833 (p) REVERT: E 778 LYS cc_start: 0.8312 (mmtm) cc_final: 0.7736 (mppt) REVERT: E 780 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: E 899 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.7093 (t0) REVERT: E 1021 GLN cc_start: 0.7258 (mp10) cc_final: 0.6890 (mp10) REVERT: E 1062 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7329 (mp) REVERT: F 200 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7719 (ttp-170) REVERT: F 216 LYS cc_start: 0.7911 (ptmt) cc_final: 0.7508 (pttm) REVERT: F 335 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7332 (ptp-170) REVERT: F 517 MET cc_start: 0.8421 (ttm) cc_final: 0.8003 (mtm) REVERT: F 559 LEU cc_start: 0.8648 (mp) cc_final: 0.8426 (mt) REVERT: F 612 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8097 (m-40) REVERT: F 735 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8030 (mtt) REVERT: F 908 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6544 (pttp) REVERT: F 951 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6896 (mmm160) REVERT: F 980 LYS cc_start: 0.8416 (ptmm) cc_final: 0.8087 (ptmm) REVERT: G 440 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7036 (tm-30) REVERT: G 622 ARG cc_start: 0.7430 (mpt180) cc_final: 0.7168 (mpt-90) REVERT: G 718 THR cc_start: 0.3742 (OUTLIER) cc_final: 0.3345 (m) REVERT: G 721 GLN cc_start: 0.1868 (OUTLIER) cc_final: 0.0253 (mm-40) REVERT: H 493 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7569 (pt0) REVERT: H 515 GLU cc_start: 0.7484 (tp30) cc_final: 0.7169 (tp30) REVERT: H 639 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8549 (tp) REVERT: H 685 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8776 (mm) REVERT: L 129 ARG cc_start: 0.0353 (mtm-85) cc_final: 0.0094 (ptp90) REVERT: L 227 CYS cc_start: 0.5244 (m) cc_final: 0.4646 (m) REVERT: L 390 THR cc_start: 0.6831 (m) cc_final: 0.6375 (t) REVERT: L 435 ARG cc_start: 0.2814 (tpt170) cc_final: 0.1502 (mpp-170) REVERT: L 471 PHE cc_start: 0.4612 (OUTLIER) cc_final: 0.4191 (p90) REVERT: L 490 ASP cc_start: 0.5099 (OUTLIER) cc_final: 0.4659 (t0) REVERT: L 565 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5744 (pp) REVERT: L 625 ARG cc_start: 0.4563 (mmm-85) cc_final: 0.4221 (mmp80) REVERT: L 637 ASN cc_start: 0.4339 (m-40) cc_final: 0.3680 (p0) REVERT: L 659 MET cc_start: 0.3261 (mmm) cc_final: 0.2717 (mmm) REVERT: L 663 MET cc_start: 0.2646 (ptt) cc_final: 0.2310 (ptt) REVERT: M 77 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6504 (pp-130) outliers start: 184 outliers final: 89 residues processed: 661 average time/residue: 1.3571 time to fit residues: 1164.0333 Evaluate side-chains 602 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 488 time to evaluate : 5.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 571 THR Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 720 CYS Chi-restraints excluded: chain E residue 775 VAL Chi-restraints excluded: chain E residue 780 GLN Chi-restraints excluded: chain E residue 804 SER Chi-restraints excluded: chain E residue 832 SER Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 899 ASN Chi-restraints excluded: chain E residue 966 ILE Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain E residue 998 MET Chi-restraints excluded: chain E residue 1062 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 200 ARG Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 335 ARG Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 466 THR Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 531 ASN Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 612 ASN Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 653 THR Chi-restraints excluded: chain F residue 712 THR Chi-restraints excluded: chain F residue 735 MET Chi-restraints excluded: chain F residue 744 MET Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 908 LYS Chi-restraints excluded: chain F residue 919 ASP Chi-restraints excluded: chain F residue 951 ARG Chi-restraints excluded: chain F residue 977 LEU Chi-restraints excluded: chain F residue 986 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 126 LYS Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 295 SER Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 669 VAL Chi-restraints excluded: chain G residue 674 THR Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain G residue 721 GLN Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain H residue 346 ASP Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 493 GLN Chi-restraints excluded: chain H residue 537 ASN Chi-restraints excluded: chain H residue 556 GLU Chi-restraints excluded: chain H residue 562 THR Chi-restraints excluded: chain H residue 620 LEU Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain H residue 665 MET Chi-restraints excluded: chain H residue 685 ILE Chi-restraints excluded: chain H residue 708 THR Chi-restraints excluded: chain H residue 859 ASP Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 287 THR Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 471 PHE Chi-restraints excluded: chain L residue 490 ASP Chi-restraints excluded: chain L residue 565 LEU Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain L residue 579 VAL Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain M residue 77 MET Chi-restraints excluded: chain M residue 103 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 354 optimal weight: 0.1980 chunk 228 optimal weight: 0.5980 chunk 341 optimal weight: 1.9990 chunk 172 optimal weight: 0.0370 chunk 112 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 363 optimal weight: 0.0870 chunk 390 optimal weight: 0.0000 chunk 283 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 450 optimal weight: 0.0670 overall best weight: 0.0778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN D 185 GLN F 69 HIS F 130 ASN F 146 GLN ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 607 GLN H 670 ASN H 836 ASN ** H 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 891 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: 0.7141 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 49059 Z= 0.146 Angle : 0.598 14.467 66750 Z= 0.297 Chirality : 0.043 0.420 7837 Planarity : 0.004 0.057 8243 Dihedral : 6.088 63.213 7976 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.98 % Favored : 94.86 % Rotamer: Outliers : 2.36 % Allowed : 23.81 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.33 (0.12), residues: 2069 sheet: 0.33 (0.15), residues: 1266 loop : -1.36 (0.12), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 98 HIS 0.005 0.001 HIS M 116 PHE 0.039 0.001 PHE A 358 TYR 0.029 0.001 TYR L 121 ARG 0.014 0.000 ARG A 467 *********************** 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 649 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 532 time to evaluate : 5.052 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: A 400 VAL cc_start: 0.8112 (t) cc_final: 0.7877 (m) REVERT: A 401 LEU cc_start: 0.7564 (mt) cc_final: 0.7192 (pp) REVERT: A 419 ASP cc_start: 0.7425 (t0) cc_final: 0.7192 (m-30) REVERT: A 425 MET cc_start: 0.7158 (tpp) cc_final: 0.6900 (tpt) REVERT: A 436 ASN cc_start: 0.6394 (m110) cc_final: 0.5871 (m110) REVERT: A 518 ARG cc_start: 0.7757 (tpp-160) cc_final: 0.7447 (mmt-90) REVERT: A 533 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7899 (mp) REVERT: A 541 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7237 (pt) REVERT: A 545 ASN cc_start: 0.8341 (m-40) cc_final: 0.8115 (m110) REVERT: B 180 PHE cc_start: 0.7782 (t80) cc_final: 0.7340 (t80) REVERT: B 341 ASN cc_start: 0.7563 (t0) cc_final: 0.7269 (t0) REVERT: C 87 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6431 (mm-30) REVERT: C 185 PHE cc_start: 0.7818 (t80) cc_final: 0.7488 (t80) REVERT: C 226 VAL cc_start: 0.7268 (m) cc_final: 0.7050 (t) REVERT: C 272 GLU cc_start: 0.7229 (tt0) cc_final: 0.7006 (mt-10) REVERT: C 275 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6729 (ppp) REVERT: C 291 MET cc_start: 0.5929 (mmt) cc_final: 0.4363 (pmm) REVERT: D 113 ILE cc_start: 0.8270 (mt) cc_final: 0.8012 (tp) REVERT: D 187 MET cc_start: 0.6930 (tpt) cc_final: 0.6689 (mmm) REVERT: D 194 MET cc_start: 0.7357 (mtt) cc_final: 0.7083 (mtt) REVERT: D 205 SER cc_start: 0.8114 (t) cc_final: 0.7259 (p) REVERT: D 247 GLN cc_start: 0.6884 (tm-30) cc_final: 0.6664 (tm-30) REVERT: D 248 MET cc_start: 0.6801 (mmm) cc_final: 0.5933 (mpm) REVERT: D 289 MET cc_start: 0.6281 (mpp) cc_final: 0.5433 (tmm) REVERT: E 685 MET cc_start: 0.7233 (ttm) cc_final: 0.6869 (ttp) REVERT: E 732 MET cc_start: 0.7241 (ppp) cc_final: 0.6959 (pp-130) REVERT: E 778 LYS cc_start: 0.8277 (mmtm) cc_final: 0.7709 (mppt) REVERT: E 780 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: E 899 ASN cc_start: 0.7211 (OUTLIER) cc_final: 0.6967 (t0) REVERT: E 1021 GLN cc_start: 0.7070 (mp10) cc_final: 0.6703 (mp10) REVERT: E 1062 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7280 (mp) REVERT: F 200 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7481 (ttp-170) REVERT: F 216 LYS cc_start: 0.7826 (ptmt) cc_final: 0.7391 (pttm) REVERT: F 302 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8512 (mm) REVERT: F 517 MET cc_start: 0.8240 (ttm) cc_final: 0.7920 (mtm) REVERT: F 612 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.8038 (m-40) REVERT: F 890 TYR cc_start: 0.7954 (t80) cc_final: 0.7728 (t80) REVERT: F 908 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6633 (pttp) REVERT: F 980 LYS cc_start: 0.8370 (ptmm) cc_final: 0.8046 (ptmm) REVERT: F 1060 LYS cc_start: 0.7666 (tppp) cc_final: 0.6832 (ttpp) REVERT: G 718 THR cc_start: 0.3877 (OUTLIER) cc_final: 0.3395 (m) REVERT: G 721 GLN cc_start: 0.1785 (OUTLIER) cc_final: 0.0242 (mm-40) REVERT: H 493 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7344 (pt0) REVERT: H 612 ASP cc_start: 0.5845 (OUTLIER) cc_final: 0.5484 (m-30) REVERT: L 129 ARG cc_start: 0.0406 (mtm-85) cc_final: 0.0141 (ptp90) REVERT: L 227 CYS cc_start: 0.5021 (m) cc_final: 0.4446 (m) REVERT: L 374 MET cc_start: 0.0557 (mmp) cc_final: 0.0006 (mmp) REVERT: L 390 THR cc_start: 0.6823 (m) cc_final: 0.6388 (t) REVERT: L 435 ARG cc_start: 0.2814 (tpt170) cc_final: 0.1638 (mpp-170) REVERT: L 471 PHE cc_start: 0.4765 (OUTLIER) cc_final: 0.4347 (p90) REVERT: L 565 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5761 (pp) REVERT: L 625 ARG cc_start: 0.4856 (mmm-85) cc_final: 0.4520 (mmp80) REVERT: L 637 ASN cc_start: 0.4253 (m-40) cc_final: 0.3628 (p0) REVERT: L 659 MET cc_start: 0.3230 (mmm) cc_final: 0.2702 (mmm) outliers start: 117 outliers final: 48 residues processed: 621 average time/residue: 1.3490 time to fit residues: 1082.8744 Evaluate side-chains 555 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 490 time to evaluate : 5.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 TYR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 530 ARG Chi-restraints excluded: chain E residue 720 CYS Chi-restraints excluded: chain E residue 780 GLN Chi-restraints excluded: chain E residue 804 SER Chi-restraints excluded: chain E residue 899 ASN Chi-restraints excluded: chain E residue 966 ILE Chi-restraints excluded: chain E residue 1062 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 200 ARG Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 466 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 612 ASN Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 712 THR Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 908 LYS Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 669 VAL Chi-restraints excluded: chain G residue 674 THR Chi-restraints excluded: chain G residue 715 LEU Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain G residue 721 GLN Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 346 ASP Chi-restraints excluded: chain H residue 493 GLN Chi-restraints excluded: chain H residue 562 THR Chi-restraints excluded: chain H residue 612 ASP Chi-restraints excluded: chain H residue 665 MET Chi-restraints excluded: chain H residue 708 THR Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 327 SER Chi-restraints excluded: chain L residue 471 PHE Chi-restraints excluded: chain L residue 556 ILE Chi-restraints excluded: chain L residue 565 LEU Chi-restraints excluded: chain L residue 571 PHE Chi-restraints excluded: chain L residue 579 VAL Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain M residue 77 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 520 optimal weight: 10.0000 chunk 548 optimal weight: 50.0000 chunk 500 optimal weight: 9.9990 chunk 533 optimal weight: 20.0000 chunk 321 optimal weight: 0.8980 chunk 232 optimal weight: 0.1980 chunk 418 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 482 optimal weight: 50.0000 chunk 504 optimal weight: 0.0470 chunk 531 optimal weight: 9.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN D 185 GLN E 450 HIS E 606 HIS E 944 HIS ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 648 HIS ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN H 670 ASN ** H 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 49059 Z= 0.308 Angle : 0.684 17.208 66750 Z= 0.341 Chirality : 0.047 0.533 7837 Planarity : 0.004 0.059 8243 Dihedral : 6.298 66.007 7974 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.72 % Favored : 94.13 % Rotamer: Outliers : 2.44 % Allowed : 24.05 % Favored : 73.51 % 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: -0.13 (0.11), residues: 5929 helix: 1.31 (0.12), residues: 2071 sheet: 0.24 (0.14), residues: 1288 loop : -1.45 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 98 HIS 0.008 0.001 HIS F 69 PHE 0.037 0.002 PHE A 358 TYR 0.029 0.002 TYR E 550 ARG 0.014 0.001 ARG A 467 *********************** 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 628 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 507 time to evaluate : 5.248 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: A 400 VAL cc_start: 0.8104 (t) cc_final: 0.7877 (m) REVERT: A 401 LEU cc_start: 0.7611 (mt) cc_final: 0.7205 (pp) REVERT: A 419 ASP cc_start: 0.7347 (t0) cc_final: 0.7111 (m-30) REVERT: A 425 MET cc_start: 0.7245 (tpp) cc_final: 0.7006 (tpt) REVERT: A 436 ASN cc_start: 0.6518 (m110) cc_final: 0.5979 (m110) REVERT: A 518 ARG cc_start: 0.7711 (tpp-160) cc_final: 0.7388 (mmt-90) REVERT: A 519 PHE cc_start: 0.6915 (OUTLIER) cc_final: 0.6231 (p90) REVERT: A 533 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7847 (mp) REVERT: A 545 ASN cc_start: 0.8392 (m-40) cc_final: 0.8137 (m110) REVERT: B 180 PHE cc_start: 0.7756 (t80) cc_final: 0.7318 (t80) REVERT: B 341 ASN cc_start: 0.7843 (t0) cc_final: 0.7629 (t0) REVERT: B 353 MET cc_start: 0.7691 (ppp) cc_final: 0.7290 (pp-130) REVERT: C 272 GLU cc_start: 0.7187 (tt0) cc_final: 0.6946 (mt-10) REVERT: C 275 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.7052 (ppp) REVERT: C 291 MET cc_start: 0.5908 (mmt) cc_final: 0.4564 (tmt) REVERT: D 113 ILE cc_start: 0.8349 (mt) cc_final: 0.8087 (tp) REVERT: D 126 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7830 (tt) REVERT: D 187 MET cc_start: 0.7048 (tpt) cc_final: 0.6773 (mmm) REVERT: D 194 MET cc_start: 0.7306 (mtt) cc_final: 0.6998 (mtt) REVERT: D 247 GLN cc_start: 0.6932 (tm-30) cc_final: 0.6718 (tm-30) REVERT: D 248 MET cc_start: 0.6740 (mmm) cc_final: 0.5930 (mpm) REVERT: D 289 MET cc_start: 0.6189 (mpp) cc_final: 0.5260 (tmm) REVERT: E 367 ASP cc_start: 0.7992 (t0) cc_final: 0.7763 (t70) REVERT: E 685 MET cc_start: 0.7573 (ttm) cc_final: 0.7290 (ttp) REVERT: E 778 LYS cc_start: 0.8318 (mmtm) cc_final: 0.7724 (mppt) REVERT: E 780 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: E 899 ASN cc_start: 0.7343 (OUTLIER) cc_final: 0.6918 (t0) REVERT: E 904 SER cc_start: 0.7408 (t) cc_final: 0.6914 (m) REVERT: E 1021 GLN cc_start: 0.7182 (mp10) cc_final: 0.6905 (mp10) REVERT: E 1062 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7372 (mp) REVERT: F 200 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7747 (ttp-170) REVERT: F 517 MET cc_start: 0.8444 (ttm) cc_final: 0.8020 (mtm) REVERT: F 612 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8182 (m-40) REVERT: F 908 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6630 (pttp) REVERT: F 980 LYS cc_start: 0.8490 (ptmm) cc_final: 0.8162 (ptmm) REVERT: F 1060 LYS cc_start: 0.7716 (tppp) cc_final: 0.6877 (ttpp) REVERT: G 718 THR cc_start: 0.3988 (OUTLIER) cc_final: 0.3526 (m) REVERT: G 721 GLN cc_start: 0.1891 (OUTLIER) cc_final: 0.0230 (mm-40) REVERT: H 493 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7620 (pt0) REVERT: H 515 GLU cc_start: 0.7718 (tp30) cc_final: 0.7339 (tp30) REVERT: H 633 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.5029 (pp-130) REVERT: L 129 ARG cc_start: 0.0440 (mtm-85) cc_final: 0.0159 (ptp90) REVERT: L 227 CYS cc_start: 0.5175 (m) cc_final: 0.4585 (m) REVERT: L 374 MET cc_start: 0.0632 (mmp) cc_final: 0.0092 (mmp) REVERT: L 390 THR cc_start: 0.6363 (m) cc_final: 0.6098 (t) REVERT: L 435 ARG cc_start: 0.2856 (tpt170) cc_final: 0.1709 (mpp-170) REVERT: L 471 PHE cc_start: 0.4718 (OUTLIER) cc_final: 0.4385 (p90) REVERT: L 625 ARG cc_start: 0.5014 (mmm-85) cc_final: 0.4489 (mmp80) REVERT: L 637 ASN cc_start: 0.4261 (m-40) cc_final: 0.3633 (p0) REVERT: L 659 MET cc_start: 0.3267 (mmm) cc_final: 0.2709 (mmm) REVERT: L 663 MET cc_start: 0.2592 (ptt) cc_final: 0.2208 (ptt) outliers start: 121 outliers final: 64 residues processed: 595 average time/residue: 1.3500 time to fit residues: 1040.4122 Evaluate side-chains 562 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 483 time to evaluate : 5.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 530 ARG Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain E residue 720 CYS Chi-restraints excluded: chain E residue 780 GLN Chi-restraints excluded: chain E residue 782 VAL Chi-restraints excluded: chain E residue 804 SER Chi-restraints excluded: chain E residue 899 ASN Chi-restraints excluded: chain E residue 966 ILE Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain E residue 998 MET Chi-restraints excluded: chain E residue 1062 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 200 ARG Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 466 THR Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 612 ASN Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 653 THR Chi-restraints excluded: chain F residue 712 THR Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 806 THR Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 908 LYS Chi-restraints excluded: chain F residue 919 ASP Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 669 VAL Chi-restraints excluded: chain G residue 674 THR Chi-restraints excluded: chain G residue 715 LEU Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain G residue 721 GLN Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain H residue 346 ASP Chi-restraints excluded: chain H residue 493 GLN Chi-restraints excluded: chain H residue 556 GLU Chi-restraints excluded: chain H residue 562 THR Chi-restraints excluded: chain H residue 620 LEU Chi-restraints excluded: chain H residue 633 MET Chi-restraints excluded: chain H residue 708 THR Chi-restraints excluded: chain H residue 859 ASP Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 471 PHE Chi-restraints excluded: chain L residue 556 ILE Chi-restraints excluded: chain L residue 579 VAL Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain M residue 77 MET 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: 10.0000 chunk 344 optimal weight: 0.6980 chunk 267 optimal weight: 3.9990 chunk 392 optimal weight: 0.9990 chunk 591 optimal weight: 8.9990 chunk 544 optimal weight: 0.0870 chunk 471 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 363 optimal weight: 8.9990 chunk 288 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN D 185 GLN E 606 HIS ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 495 HIS H 607 GLN H 670 ASN H 843 GLN ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 49059 Z= 0.185 Angle : 0.631 17.152 66750 Z= 0.314 Chirality : 0.044 0.489 7837 Planarity : 0.004 0.066 8243 Dihedral : 6.050 60.369 7974 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.48 % Favored : 94.42 % Rotamer: Outliers : 1.89 % Allowed : 24.68 % Favored : 73.43 % 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: -0.12 (0.11), residues: 5929 helix: 1.34 (0.12), residues: 2069 sheet: 0.22 (0.15), residues: 1258 loop : -1.44 (0.12), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP B 98 HIS 0.006 0.001 HIS H 894 PHE 0.038 0.001 PHE A 358 TYR 0.028 0.001 TYR E 550 ARG 0.016 0.000 ARG A 467 ********************** 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 594 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 500 time to evaluate : 5.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 VAL cc_start: 0.8093 (t) cc_final: 0.7869 (m) REVERT: A 401 LEU cc_start: 0.7593 (mt) cc_final: 0.7197 (pp) REVERT: A 419 ASP cc_start: 0.7340 (t0) cc_final: 0.7121 (m-30) REVERT: A 425 MET cc_start: 0.7186 (tpp) cc_final: 0.6948 (tpt) REVERT: A 436 ASN cc_start: 0.6504 (m110) cc_final: 0.6018 (m110) REVERT: A 518 ARG cc_start: 0.7751 (tpp-160) cc_final: 0.7406 (mmt-90) REVERT: A 533 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7742 (mp) REVERT: A 545 ASN cc_start: 0.8333 (m-40) cc_final: 0.8105 (m110) REVERT: B 155 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6373 (t80) REVERT: B 180 PHE cc_start: 0.7741 (t80) cc_final: 0.7287 (t80) REVERT: B 203 TRP cc_start: 0.6384 (OUTLIER) cc_final: 0.6005 (m-10) REVERT: B 341 ASN cc_start: 0.7730 (t0) cc_final: 0.7492 (t0) REVERT: B 353 MET cc_start: 0.7654 (ppp) cc_final: 0.7442 (pp-130) REVERT: C 272 GLU cc_start: 0.7194 (tt0) cc_final: 0.6984 (mt-10) REVERT: C 280 ARG cc_start: 0.7241 (mtt180) cc_final: 0.6915 (mmp80) REVERT: C 291 MET cc_start: 0.5932 (mmt) cc_final: 0.4564 (tmt) REVERT: D 113 ILE cc_start: 0.8314 (mt) cc_final: 0.8063 (tp) REVERT: D 187 MET cc_start: 0.7026 (tpt) cc_final: 0.6762 (mmm) REVERT: D 194 MET cc_start: 0.7306 (mtt) cc_final: 0.7028 (mtt) REVERT: D 247 GLN cc_start: 0.6964 (tm-30) cc_final: 0.6717 (tm-30) REVERT: D 248 MET cc_start: 0.6805 (mmm) cc_final: 0.5908 (mpm) REVERT: D 289 MET cc_start: 0.6235 (mpp) cc_final: 0.5280 (tmm) REVERT: E 367 ASP cc_start: 0.7943 (t0) cc_final: 0.7730 (t70) REVERT: E 579 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7143 (mt-10) REVERT: E 685 MET cc_start: 0.7334 (ttm) cc_final: 0.7130 (ttp) REVERT: E 778 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7687 (mppt) REVERT: E 780 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: E 899 ASN cc_start: 0.7329 (OUTLIER) cc_final: 0.6972 (t0) REVERT: E 904 SER cc_start: 0.7382 (t) cc_final: 0.6888 (m) REVERT: E 1021 GLN cc_start: 0.7069 (mp10) cc_final: 0.6717 (mp10) REVERT: E 1062 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7353 (mp) REVERT: F 128 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7981 (tp-100) REVERT: F 200 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7640 (ttp-170) REVERT: F 302 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8634 (mm) REVERT: F 517 MET cc_start: 0.8320 (ttm) cc_final: 0.7965 (mtm) REVERT: F 612 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8086 (m-40) REVERT: F 908 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6656 (pttp) REVERT: F 980 LYS cc_start: 0.8489 (ptmm) cc_final: 0.8152 (ptmm) REVERT: F 1060 LYS cc_start: 0.7699 (tppp) cc_final: 0.6863 (ttpp) REVERT: G 718 THR cc_start: 0.3882 (OUTLIER) cc_final: 0.3394 (m) REVERT: H 493 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7474 (pt0) REVERT: H 515 GLU cc_start: 0.7617 (tp30) cc_final: 0.7308 (tp30) REVERT: H 633 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.4789 (pp-130) REVERT: L 129 ARG cc_start: 0.0405 (mtm-85) cc_final: 0.0175 (ptp90) REVERT: L 227 CYS cc_start: 0.5034 (m) cc_final: 0.4469 (m) REVERT: L 374 MET cc_start: 0.0609 (mmp) cc_final: 0.0071 (mmp) REVERT: L 390 THR cc_start: 0.6635 (m) cc_final: 0.6284 (t) REVERT: L 435 ARG cc_start: 0.3029 (tpt170) cc_final: 0.1722 (mpp-170) REVERT: L 471 PHE cc_start: 0.4764 (OUTLIER) cc_final: 0.4402 (p90) REVERT: L 565 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5796 (pp) REVERT: L 625 ARG cc_start: 0.4993 (mmm-85) cc_final: 0.4463 (mmp80) REVERT: L 637 ASN cc_start: 0.4255 (m-40) cc_final: 0.3639 (p0) REVERT: L 659 MET cc_start: 0.3114 (mmm) cc_final: 0.2605 (mmm) REVERT: L 663 MET cc_start: 0.2370 (ptt) cc_final: 0.1948 (ptt) outliers start: 94 outliers final: 59 residues processed: 575 average time/residue: 1.4616 time to fit residues: 1086.7654 Evaluate side-chains 551 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 476 time to evaluate : 5.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 530 ARG Chi-restraints excluded: chain E residue 720 CYS Chi-restraints excluded: chain E residue 780 GLN Chi-restraints excluded: chain E residue 804 SER Chi-restraints excluded: chain E residue 899 ASN Chi-restraints excluded: chain E residue 966 ILE Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain E residue 998 MET Chi-restraints excluded: chain E residue 1062 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 128 GLN Chi-restraints excluded: chain F residue 200 ARG Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 466 THR Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 612 ASN Chi-restraints excluded: chain F residue 632 HIS Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 653 THR Chi-restraints excluded: chain F residue 712 THR Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 908 LYS Chi-restraints excluded: chain F residue 919 ASP Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 669 VAL Chi-restraints excluded: chain G residue 674 THR Chi-restraints excluded: chain G residue 715 LEU Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain H residue 346 ASP Chi-restraints excluded: chain H residue 493 GLN Chi-restraints excluded: chain H residue 537 ASN Chi-restraints excluded: chain H residue 562 THR Chi-restraints excluded: chain H residue 633 MET Chi-restraints excluded: chain H residue 708 THR Chi-restraints excluded: chain H residue 859 ASP Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 460 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 471 PHE Chi-restraints excluded: chain L residue 556 ILE Chi-restraints excluded: chain L residue 565 LEU Chi-restraints excluded: chain L residue 571 PHE Chi-restraints excluded: chain L residue 579 VAL Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain M residue 77 MET 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: 1.9990 chunk 144 optimal weight: 1.9990 chunk 434 optimal weight: 0.2980 chunk 69 optimal weight: 5.9990 chunk 130 optimal weight: 0.0470 chunk 471 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 484 optimal weight: 30.0000 chunk 59 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN A 570 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 HIS D 151 GLN D 185 GLN ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 670 ASN ** H 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 891 ASN ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.191354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.127908 restraints weight = 66977.372| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.74 r_work: 0.3334 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 49059 Z= 0.263 Angle : 0.670 16.784 66750 Z= 0.333 Chirality : 0.046 0.542 7837 Planarity : 0.004 0.069 8243 Dihedral : 6.074 60.755 7971 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.89 % Favored : 93.96 % Rotamer: Outliers : 2.50 % Allowed : 24.28 % Favored : 73.23 % 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: -0.19 (0.11), residues: 5929 helix: 1.32 (0.12), residues: 2074 sheet: 0.17 (0.14), residues: 1265 loop : -1.51 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 861 HIS 0.007 0.001 HIS F 69 PHE 0.050 0.002 PHE C 278 TYR 0.031 0.002 TYR E 550 ARG 0.015 0.001 ARG A 467 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19710.41 seconds wall clock time: 349 minutes 53.14 seconds (20993.14 seconds total)