Starting phenix.real_space_refine on Thu Feb 22 10:12:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9q_31036/02_2024/7e9q_31036.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9q_31036/02_2024/7e9q_31036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9q_31036/02_2024/7e9q_31036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9q_31036/02_2024/7e9q_31036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9q_31036/02_2024/7e9q_31036.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9q_31036/02_2024/7e9q_31036.pdb" } resolution = 3.65 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 21504 2.51 5 N 5622 2.21 5 O 6603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 737": "OD1" <-> "OD2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 84": "OE1" <-> "OE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 166": "OE1" <-> "OE2" Residue "L TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 118": "OD1" <-> "OD2" Residue "H PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 225": "OD1" <-> "OD2" Residue "X TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 128": "OE1" <-> "OE2" Residue "X TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 19": "NH1" <-> "NH2" Residue "Y ASP 31": "OD1" <-> "OD2" Residue "Y ASP 73": "OD1" <-> "OD2" Residue "Y TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 84": "NH1" <-> "NH2" Residue "Y GLU 89": "OE1" <-> "OE2" Residue "Y TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 127": "OD1" <-> "OD2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33876 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "A" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "C" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "L" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "X" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "Y" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "E" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "F" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 17.65, per 1000 atoms: 0.52 Number of scatterers: 33876 At special positions: 0 Unit cell: (191.625, 205.86, 227.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 147 16.00 O 6603 8.00 N 5622 7.00 C 21504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.06 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 157 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 93 " distance=2.03 Simple disulfide: pdb=" SG CYS X 139 " - pdb=" SG CYS X 199 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 157 " - pdb=" SG CYS Y 213 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.05 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 199 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 213 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A1098 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B1098 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " Time building additional restraints: 12.83 Conformation dependent library (CDL) restraints added in 5.9 seconds 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 65 sheets defined 18.4% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.752A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.584A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.839A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.731A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.587A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.536A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.031A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.933A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.757A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.074A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.967A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.079A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.540A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 967 removed outlier: 4.056A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.085A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.859A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 4.159A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.255A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.941A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.573A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.641A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.663A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.613A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.617A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.503A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.557A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.839A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.718A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.757A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.556A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.867A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 188 through 194 removed outlier: 4.406A pdb=" N GLU L 192 " --> pdb=" O LYS L 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 173 through 175 No H-bonds generated for 'chain 'H' and resid 173 through 175' Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'X' and resid 84 through 88 Processing helix chain 'X' and resid 126 through 132 Processing helix chain 'Y' and resid 87 through 91 removed outlier: 3.982A pdb=" N THR Y 91 " --> pdb=" O ALA Y 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 removed outlier: 4.122A pdb=" N GLU E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.524A pdb=" N ASP F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.667A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.415A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.065A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.708A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.488A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 327 through 328 removed outlier: 3.708A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.888A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.614A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AB3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AB4, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.520A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.952A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AB7, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AB8, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.703A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.296A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AC4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.925A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC6, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AC7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC8, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.701A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.175A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.504A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.834A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.252A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.548A pdb=" N ALA C 694 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.713A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.713A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AE2, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AE3, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AE4, first strand: chain 'L' and resid 58 through 59 removed outlier: 4.944A pdb=" N SER L 48 " --> pdb=" O LYS L 44 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS L 44 " --> pdb=" O SER L 48 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU L 38 " --> pdb=" O TYR L 54 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.925A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 158 through 160 removed outlier: 4.017A pdb=" N TRP L 153 " --> pdb=" O GLN L 160 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE9, first strand: chain 'H' and resid 57 through 60 removed outlier: 7.002A pdb=" N GLY H 50 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR H 60 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL H 48 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 137 through 141 removed outlier: 6.393A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 137 through 141 removed outlier: 6.393A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 168 through 171 Processing sheet with id=AF4, first strand: chain 'X' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'X' and resid 50 through 54 removed outlier: 6.357A pdb=" N TRP X 40 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TYR X 54 " --> pdb=" O LEU X 38 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU X 38 " --> pdb=" O TYR X 54 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 119 through 123 removed outlier: 5.408A pdb=" N SER X 136 " --> pdb=" O LEU X 186 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU X 186 " --> pdb=" O SER X 136 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL X 138 " --> pdb=" O LEU X 184 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU X 184 " --> pdb=" O VAL X 138 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU X 140 " --> pdb=" O SER X 182 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER X 182 " --> pdb=" O LEU X 140 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASN X 142 " --> pdb=" O LEU X 180 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU X 180 " --> pdb=" O ASN X 142 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER X 179 " --> pdb=" O GLU X 170 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU X 170 " --> pdb=" O SER X 179 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER X 181 " --> pdb=" O VAL X 168 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL X 168 " --> pdb=" O SER X 181 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR X 183 " --> pdb=" O GLU X 166 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU X 166 " --> pdb=" O THR X 183 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 159 through 160 removed outlier: 4.521A pdb=" N TRP X 153 " --> pdb=" O GLN X 160 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'Y' and resid 45 through 51 removed outlier: 6.758A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLY Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET Y 34 " --> pdb=" O GLY Y 50 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Y' and resid 137 through 141 removed outlier: 6.512A pdb=" N TYR Y 193 " --> pdb=" O ASP Y 161 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 137 through 141 removed outlier: 6.512A pdb=" N TYR Y 193 " --> pdb=" O ASP Y 161 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y' and resid 167 through 171 removed outlier: 4.336A pdb=" N TYR Y 211 " --> pdb=" O VAL Y 228 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=AG5, first strand: chain 'E' and resid 58 through 59 removed outlier: 6.456A pdb=" N TRP E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 119 through 123 removed outlier: 3.710A pdb=" N VAL E 138 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR E 178 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 150 through 154 removed outlier: 4.018A pdb=" N LYS E 150 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AG9, first strand: chain 'F' and resid 45 through 51 removed outlier: 6.445A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS F 98 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL F 119 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.850A pdb=" N SER F 137 " --> pdb=" O LYS F 160 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N CYS F 157 " --> pdb=" O SER F 197 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER F 197 " --> pdb=" O CYS F 157 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER F 196 " --> pdb=" O PHE F 183 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 168 through 170 1314 hydrogen bonds defined for protein. 3495 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: 15.04 Time building geometry restraints manager: 13.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5562 1.30 - 1.43: 9381 1.43 - 1.57: 19509 1.57 - 1.70: 0 1.70 - 1.83: 189 Bond restraints: 34641 Sorted by residual: bond pdb=" CA SER A 816 " pdb=" CB SER A 816 " ideal model delta sigma weight residual 1.538 1.463 0.075 1.29e-02 6.01e+03 3.36e+01 bond pdb=" C PRO A 897 " pdb=" O PRO A 897 " ideal model delta sigma weight residual 1.233 1.166 0.067 1.16e-02 7.43e+03 3.30e+01 bond pdb=" C7 NAG A1305 " pdb=" N2 NAG A1305 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C7 NAG C1304 " pdb=" N2 NAG C1304 " ideal model delta sigma weight residual 1.346 1.457 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C7 NAG A1304 " pdb=" N2 NAG A1304 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 34636 not shown) Histogram of bond angle deviations from ideal: 97.32 - 104.67: 680 104.67 - 112.03: 16799 112.03 - 119.38: 11324 119.38 - 126.73: 17959 126.73 - 134.08: 386 Bond angle restraints: 47148 Sorted by residual: angle pdb=" N ILE X 111 " pdb=" CA ILE X 111 " pdb=" C ILE X 111 " ideal model delta sigma weight residual 110.72 119.54 -8.82 1.01e+00 9.80e-01 7.63e+01 angle pdb=" CA PRO A 897 " pdb=" C PRO A 897 " pdb=" O PRO A 897 " ideal model delta sigma weight residual 121.34 112.69 8.65 1.14e+00 7.69e-01 5.76e+01 angle pdb=" CA PRO A 897 " pdb=" C PRO A 897 " pdb=" N PHE A 898 " ideal model delta sigma weight residual 115.56 124.99 -9.43 1.27e+00 6.20e-01 5.51e+01 angle pdb=" CA PHE A 888 " pdb=" CB PHE A 888 " pdb=" CG PHE A 888 " ideal model delta sigma weight residual 113.80 120.51 -6.71 1.00e+00 1.00e+00 4.50e+01 angle pdb=" N PRO A 897 " pdb=" CA PRO A 897 " pdb=" CB PRO A 897 " ideal model delta sigma weight residual 103.31 97.35 5.96 8.90e-01 1.26e+00 4.48e+01 ... (remaining 47143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 19729 24.08 - 48.16: 961 48.16 - 72.24: 160 72.24 - 96.32: 70 96.32 - 120.40: 107 Dihedral angle restraints: 21027 sinusoidal: 8475 harmonic: 12552 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 177.80 -84.80 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -1.99 -84.01 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS H 157 " pdb=" SG CYS H 157 " pdb=" SG CYS H 213 " pdb=" CB CYS H 213 " ideal model delta sinusoidal sigma weight residual 93.00 176.33 -83.33 1 1.00e+01 1.00e-02 8.48e+01 ... (remaining 21024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4891 0.091 - 0.181: 486 0.181 - 0.272: 40 0.272 - 0.362: 13 0.362 - 0.453: 3 Chirality restraints: 5433 Sorted by residual: chirality pdb=" CB VAL B 524 " pdb=" CA VAL B 524 " pdb=" CG1 VAL B 524 " pdb=" CG2 VAL B 524 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA PHE C 338 " pdb=" N PHE C 338 " pdb=" C PHE C 338 " pdb=" CB PHE C 338 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 5430 not shown) Planarity restraints: 6099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 938 " 0.021 2.00e-02 2.50e+03 4.14e-02 1.72e+01 pdb=" C LEU B 938 " -0.072 2.00e-02 2.50e+03 pdb=" O LEU B 938 " 0.027 2.00e-02 2.50e+03 pdb=" N SER B 939 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 887 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C THR B 887 " -0.067 2.00e-02 2.50e+03 pdb=" O THR B 887 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE B 888 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 84 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLU E 84 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU E 84 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA E 85 " 0.018 2.00e-02 2.50e+03 ... (remaining 6096 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3535 2.75 - 3.29: 34221 3.29 - 3.82: 54454 3.82 - 4.36: 63463 4.36 - 4.90: 108003 Nonbonded interactions: 263676 Sorted by model distance: nonbonded pdb=" OH TYR A 369 " pdb=" O PRO A 384 " model vdw 2.209 2.440 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.210 2.440 nonbonded pdb=" OG SER X 70 " pdb=" OG1 THR X 77 " model vdw 2.210 2.440 nonbonded pdb=" OG SER C 359 " pdb=" OD1 ASN C 394 " model vdw 2.222 2.440 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.222 2.440 ... (remaining 263671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'Y' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.030 Extract box with map and model: 9.430 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 86.740 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.250 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 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 : 0.007 0.115 34641 Z= 0.468 Angle : 0.930 11.431 47148 Z= 0.558 Chirality : 0.057 0.453 5433 Planarity : 0.006 0.068 6072 Dihedral : 17.925 120.402 12816 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.27 % Allowed : 1.36 % Favored : 98.38 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.33 % 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: -2.42 (0.12), residues: 4266 helix: 0.11 (0.20), residues: 668 sheet: -1.24 (0.14), residues: 1198 loop : -2.39 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP Y 36 HIS 0.007 0.001 HIS B1048 PHE 0.038 0.002 PHE A 888 TYR 0.025 0.002 TYR C 674 ARG 0.010 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 323 time to evaluate : 3.984 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 358 ILE cc_start: 0.7267 (mp) cc_final: 0.6012 (mm) REVERT: C 338 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7716 (t80) REVERT: H 134 LYS cc_start: 0.3647 (ttpp) cc_final: 0.3101 (mttt) REVERT: H 160 LYS cc_start: 0.2854 (mttm) cc_final: 0.1804 (pttm) REVERT: H 212 ILE cc_start: 0.1480 (OUTLIER) cc_final: 0.0726 (mt) REVERT: E 174 LYS cc_start: 0.3081 (mttt) cc_final: 0.2149 (pttt) REVERT: F 43 LYS cc_start: 0.3421 (mmtm) cc_final: 0.2126 (tmtt) outliers start: 10 outliers final: 1 residues processed: 332 average time/residue: 0.4892 time to fit residues: 259.5886 Evaluate side-chains 195 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain H residue 212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 7.9990 chunk 325 optimal weight: 30.0000 chunk 180 optimal weight: 0.8980 chunk 111 optimal weight: 20.0000 chunk 219 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 chunk 336 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 389 optimal weight: 30.0000 overall best weight: 3.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 1 GLN Y 181 HIS ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 34641 Z= 0.356 Angle : 0.745 9.648 47148 Z= 0.378 Chirality : 0.051 0.369 5433 Planarity : 0.005 0.062 6072 Dihedral : 14.758 112.188 5201 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 1.33 % Allowed : 9.50 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -2.20 (0.12), residues: 4266 helix: 0.61 (0.20), residues: 669 sheet: -1.07 (0.14), residues: 1183 loop : -2.36 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Y 47 HIS 0.005 0.001 HIS B1048 PHE 0.030 0.002 PHE B1121 TYR 0.027 0.002 TYR C1067 ARG 0.009 0.001 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 202 time to evaluate : 3.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7591 (p0) REVERT: B 660 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: H 102 MET cc_start: 0.4744 (pmm) cc_final: 0.4522 (pmm) REVERT: H 134 LYS cc_start: 0.3391 (ttpp) cc_final: 0.2984 (mttt) REVERT: H 160 LYS cc_start: 0.2801 (mttm) cc_final: 0.1665 (pttm) REVERT: X 175 ASP cc_start: 0.3486 (OUTLIER) cc_final: 0.3097 (m-30) REVERT: Y 32 TYR cc_start: 0.7703 (m-80) cc_final: 0.7500 (m-80) REVERT: E 174 LYS cc_start: 0.3234 (mttt) cc_final: 0.2227 (pttt) REVERT: F 43 LYS cc_start: 0.3507 (mmtm) cc_final: 0.2180 (tmtt) outliers start: 50 outliers final: 26 residues processed: 240 average time/residue: 0.5135 time to fit residues: 202.7546 Evaluate side-chains 199 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 3.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain X residue 175 ASP Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 324 optimal weight: 20.0000 chunk 265 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 390 optimal weight: 8.9990 chunk 421 optimal weight: 30.0000 chunk 347 optimal weight: 7.9990 chunk 387 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 chunk 313 optimal weight: 40.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 755 GLN ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN C 928 ASN C1106 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 HIS X 95 GLN X 165 GLN Y 1 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.171 34641 Z= 0.511 Angle : 0.806 10.066 47148 Z= 0.413 Chirality : 0.053 0.399 5433 Planarity : 0.006 0.058 6072 Dihedral : 11.834 111.814 5198 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 3.38 % Allowed : 13.15 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -2.35 (0.12), residues: 4266 helix: 0.32 (0.19), residues: 667 sheet: -1.07 (0.14), residues: 1181 loop : -2.47 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.005 0.001 HIS B1048 PHE 0.040 0.003 PHE B1121 TYR 0.035 0.002 TYR B 170 ARG 0.007 0.001 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 178 time to evaluate : 4.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 660 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7261 (m-80) REVERT: B 719 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8331 (m) REVERT: B 1031 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: B 1089 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: C 954 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7135 (mt0) REVERT: H 134 LYS cc_start: 0.3185 (ttpp) cc_final: 0.2408 (ptpt) REVERT: H 160 LYS cc_start: 0.3139 (mttm) cc_final: 0.1974 (pttm) REVERT: X 175 ASP cc_start: 0.3423 (OUTLIER) cc_final: 0.3027 (m-30) REVERT: E 174 LYS cc_start: 0.3298 (mttt) cc_final: 0.2264 (pttt) REVERT: F 43 LYS cc_start: 0.3324 (mmtm) cc_final: 0.1933 (tmtt) outliers start: 127 outliers final: 73 residues processed: 293 average time/residue: 0.4584 time to fit residues: 222.5949 Evaluate side-chains 241 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 162 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 111 ILE Chi-restraints excluded: chain X residue 175 ASP Chi-restraints excluded: chain X residue 190 ASP Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 198 VAL Chi-restraints excluded: chain Y residue 215 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 40.0000 chunk 293 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 186 optimal weight: 0.8980 chunk 262 optimal weight: 0.9980 chunk 391 optimal weight: 50.0000 chunk 414 optimal weight: 40.0000 chunk 204 optimal weight: 10.0000 chunk 371 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 34641 Z= 0.338 Angle : 0.703 10.275 47148 Z= 0.358 Chirality : 0.049 0.290 5433 Planarity : 0.005 0.055 6072 Dihedral : 9.919 109.084 5198 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.59 % Allowed : 15.04 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -2.22 (0.12), residues: 4266 helix: 0.64 (0.20), residues: 672 sheet: -1.08 (0.14), residues: 1199 loop : -2.41 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.005 0.001 HIS B1048 PHE 0.033 0.002 PHE H 163 TYR 0.024 0.002 TYR C1067 ARG 0.005 0.000 ARG H 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 191 time to evaluate : 3.655 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: B 660 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.7260 (m-80) REVERT: B 719 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8373 (m) REVERT: B 977 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7826 (pp) REVERT: B 1089 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: B 1119 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8653 (p0) REVERT: C 945 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8452 (pp) REVERT: C 954 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7125 (mt0) REVERT: H 134 LYS cc_start: 0.2699 (ttpp) cc_final: 0.1834 (ptpt) REVERT: H 160 LYS cc_start: 0.3187 (mttm) cc_final: 0.1913 (pttm) REVERT: X 175 ASP cc_start: 0.3200 (OUTLIER) cc_final: 0.2970 (m-30) REVERT: E 35 TYR cc_start: 0.2377 (OUTLIER) cc_final: 0.1539 (t80) REVERT: E 174 LYS cc_start: 0.3275 (mttt) cc_final: 0.2244 (pttt) REVERT: F 43 LYS cc_start: 0.3293 (mmtm) cc_final: 0.1942 (tmtt) outliers start: 135 outliers final: 89 residues processed: 316 average time/residue: 0.4532 time to fit residues: 238.9618 Evaluate side-chains 265 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 167 time to evaluate : 3.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 111 ILE Chi-restraints excluded: chain X residue 175 ASP Chi-restraints excluded: chain X residue 190 ASP Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 141 LEU Chi-restraints excluded: chain Y residue 215 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 308 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 353 optimal weight: 40.0000 chunk 286 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 372 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A1142 GLN C 218 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 1 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.154 34641 Z= 0.470 Angle : 0.762 10.054 47148 Z= 0.391 Chirality : 0.051 0.303 5433 Planarity : 0.005 0.056 6072 Dihedral : 9.492 108.766 5198 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 4.29 % Allowed : 16.61 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -2.32 (0.12), residues: 4266 helix: 0.42 (0.20), residues: 666 sheet: -1.10 (0.14), residues: 1185 loop : -2.44 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 36 HIS 0.005 0.001 HIS X 194 PHE 0.036 0.002 PHE B1121 TYR 0.030 0.002 TYR B 170 ARG 0.009 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 177 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 660 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: B 719 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8437 (m) REVERT: B 977 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7855 (pp) REVERT: B 1031 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: B 1089 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: B 1119 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8594 (p0) REVERT: A 197 ILE cc_start: 0.5714 (OUTLIER) cc_final: 0.5504 (mt) REVERT: A 392 PHE cc_start: 0.6683 (OUTLIER) cc_final: 0.6149 (m-80) REVERT: C 497 PHE cc_start: 0.5254 (OUTLIER) cc_final: 0.4670 (m-10) REVERT: C 945 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8295 (pp) REVERT: C 954 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7131 (mt0) REVERT: H 126 VAL cc_start: 0.4919 (t) cc_final: 0.4370 (p) REVERT: H 134 LYS cc_start: 0.2716 (ttpp) cc_final: 0.1782 (ptpt) REVERT: H 160 LYS cc_start: 0.3107 (mttm) cc_final: 0.1826 (pttm) REVERT: Y 101 GLU cc_start: 0.5749 (OUTLIER) cc_final: 0.4619 (mp0) REVERT: Y 120 TRP cc_start: 0.5261 (OUTLIER) cc_final: 0.5041 (m-90) REVERT: E 21 ILE cc_start: 0.3053 (OUTLIER) cc_final: 0.2564 (mt) REVERT: E 174 LYS cc_start: 0.3300 (mttt) cc_final: 0.2266 (pttt) REVERT: F 43 LYS cc_start: 0.3339 (mmtm) cc_final: 0.1950 (tmtt) outliers start: 161 outliers final: 112 residues processed: 325 average time/residue: 0.4613 time to fit residues: 249.7238 Evaluate side-chains 293 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 167 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 190 ASP Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain Y residue 120 TRP Chi-restraints excluded: chain Y residue 141 LEU Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 198 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 20.0000 chunk 373 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 243 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 415 optimal weight: 1.9990 chunk 344 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 217 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 129 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 34641 Z= 0.268 Angle : 0.661 9.859 47148 Z= 0.335 Chirality : 0.047 0.263 5433 Planarity : 0.005 0.058 6072 Dihedral : 8.693 105.531 5198 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.59 % Allowed : 18.02 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -2.09 (0.12), residues: 4266 helix: 0.79 (0.20), residues: 669 sheet: -0.98 (0.14), residues: 1197 loop : -2.34 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 36 HIS 0.006 0.001 HIS B1048 PHE 0.030 0.002 PHE B 135 TYR 0.021 0.002 TYR C1067 ARG 0.009 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 180 time to evaluate : 3.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 719 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8483 (m) REVERT: B 977 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7795 (pp) REVERT: B 1031 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: B 1119 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8595 (p0) REVERT: A 392 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6272 (m-80) REVERT: A 708 SER cc_start: 0.7860 (OUTLIER) cc_final: 0.7474 (m) REVERT: C 497 PHE cc_start: 0.5146 (OUTLIER) cc_final: 0.4671 (m-10) REVERT: C 954 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7187 (mt0) REVERT: C 962 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8599 (tt) REVERT: C 983 ARG cc_start: 0.7193 (ptm160) cc_final: 0.6987 (mtm180) REVERT: C 1063 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8323 (pp) REVERT: C 1107 ARG cc_start: 0.7905 (ttm170) cc_final: 0.7569 (mtt90) REVERT: H 126 VAL cc_start: 0.5028 (t) cc_final: 0.4477 (p) REVERT: H 134 LYS cc_start: 0.2703 (ttpp) cc_final: 0.1891 (ptpt) REVERT: H 160 LYS cc_start: 0.3060 (mttm) cc_final: 0.1833 (pttm) REVERT: Y 101 GLU cc_start: 0.5643 (OUTLIER) cc_final: 0.4658 (mp0) REVERT: Y 120 TRP cc_start: 0.5185 (OUTLIER) cc_final: 0.4916 (m-90) REVERT: E 21 ILE cc_start: 0.2962 (OUTLIER) cc_final: 0.2255 (mm) REVERT: E 35 TYR cc_start: 0.2868 (OUTLIER) cc_final: 0.2005 (t80) REVERT: E 174 LYS cc_start: 0.3263 (mttt) cc_final: 0.2248 (pttt) REVERT: F 43 LYS cc_start: 0.3449 (mmtm) cc_final: 0.2074 (tmtt) outliers start: 135 outliers final: 90 residues processed: 301 average time/residue: 0.4466 time to fit residues: 223.2963 Evaluate side-chains 274 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 170 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 190 ASP Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain Y residue 120 TRP Chi-restraints excluded: chain Y residue 141 LEU Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 198 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 40.0000 chunk 46 optimal weight: 2.9990 chunk 236 optimal weight: 30.0000 chunk 303 optimal weight: 10.0000 chunk 234 optimal weight: 8.9990 chunk 349 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 413 optimal weight: 0.5980 chunk 258 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 804 GLN ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 34641 Z= 0.282 Angle : 0.659 10.070 47148 Z= 0.334 Chirality : 0.047 0.271 5433 Planarity : 0.005 0.059 6072 Dihedral : 8.360 105.538 5198 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 3.83 % Allowed : 18.80 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -2.05 (0.12), residues: 4266 helix: 0.83 (0.20), residues: 663 sheet: -0.95 (0.14), residues: 1209 loop : -2.32 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 36 HIS 0.006 0.001 HIS E 31 PHE 0.036 0.002 PHE H 163 TYR 0.021 0.002 TYR C1067 ARG 0.006 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 178 time to evaluate : 3.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 ARG cc_start: 0.6440 (tpm170) cc_final: 0.6226 (tpp-160) REVERT: B 319 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6872 (ttt180) REVERT: B 719 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8481 (m) REVERT: B 901 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: B 977 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7805 (pp) REVERT: B 1031 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: B 1119 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8418 (p0) REVERT: A 392 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6287 (m-80) REVERT: A 708 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7548 (m) REVERT: C 200 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.6336 (t80) REVERT: C 954 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7136 (mt0) REVERT: C 962 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8682 (tt) REVERT: C 1107 ARG cc_start: 0.7936 (ttm170) cc_final: 0.7604 (mtt90) REVERT: L 87 ASP cc_start: 0.4264 (m-30) cc_final: 0.3903 (m-30) REVERT: H 134 LYS cc_start: 0.2670 (ttpp) cc_final: 0.1891 (ptpt) REVERT: H 160 LYS cc_start: 0.2987 (mttm) cc_final: 0.1864 (pttm) REVERT: Y 101 GLU cc_start: 0.5577 (OUTLIER) cc_final: 0.4573 (mp0) REVERT: Y 117 MET cc_start: 0.4602 (OUTLIER) cc_final: 0.3969 (mmt) REVERT: Y 120 TRP cc_start: 0.5320 (OUTLIER) cc_final: 0.5015 (m-90) REVERT: E 21 ILE cc_start: 0.3377 (OUTLIER) cc_final: 0.2635 (mm) REVERT: E 35 TYR cc_start: 0.2865 (OUTLIER) cc_final: 0.2013 (t80) REVERT: E 174 LYS cc_start: 0.3257 (mttt) cc_final: 0.2240 (pttt) REVERT: F 43 LYS cc_start: 0.3355 (mmtm) cc_final: 0.2018 (tmtt) outliers start: 144 outliers final: 112 residues processed: 309 average time/residue: 0.4390 time to fit residues: 225.9560 Evaluate side-chains 292 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 164 time to evaluate : 3.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 102 THR Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain Y residue 117 MET Chi-restraints excluded: chain Y residue 120 TRP Chi-restraints excluded: chain Y residue 141 LEU Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 198 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 262 optimal weight: 0.0770 chunk 281 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 325 optimal weight: 10.0000 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 644 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN C1106 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34641 Z= 0.218 Angle : 0.627 10.455 47148 Z= 0.317 Chirality : 0.046 0.250 5433 Planarity : 0.005 0.062 6072 Dihedral : 7.949 104.153 5198 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.59 % Allowed : 19.33 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.12), residues: 4266 helix: 1.09 (0.20), residues: 657 sheet: -0.85 (0.15), residues: 1207 loop : -2.22 (0.12), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 36 HIS 0.006 0.001 HIS C1048 PHE 0.034 0.002 PHE H 163 TYR 0.022 0.001 TYR A 495 ARG 0.013 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 182 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 317 ASN cc_start: 0.7888 (p0) cc_final: 0.7578 (p0) REVERT: B 719 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8473 (m) REVERT: B 901 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: B 977 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7763 (pp) REVERT: B 1031 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: B 1119 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8335 (p0) REVERT: A 392 PHE cc_start: 0.6969 (OUTLIER) cc_final: 0.6369 (m-80) REVERT: A 697 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7134 (ttp) REVERT: A 708 SER cc_start: 0.8039 (OUTLIER) cc_final: 0.7613 (m) REVERT: C 200 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.6219 (t80) REVERT: C 497 PHE cc_start: 0.5120 (OUTLIER) cc_final: 0.4579 (m-10) REVERT: C 954 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7182 (mt0) REVERT: C 962 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8761 (tt) REVERT: C 1063 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8246 (pp) REVERT: C 1107 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7528 (mtt90) REVERT: L 87 ASP cc_start: 0.4261 (m-30) cc_final: 0.3816 (m-30) REVERT: H 160 LYS cc_start: 0.2849 (mttm) cc_final: 0.1737 (pttm) REVERT: Y 101 GLU cc_start: 0.5345 (OUTLIER) cc_final: 0.4406 (mp0) REVERT: Y 117 MET cc_start: 0.4468 (OUTLIER) cc_final: 0.3893 (mmt) REVERT: E 35 TYR cc_start: 0.2811 (OUTLIER) cc_final: 0.1929 (t80) REVERT: E 174 LYS cc_start: 0.3234 (mttt) cc_final: 0.2218 (pttt) REVERT: F 43 LYS cc_start: 0.3436 (mmtm) cc_final: 0.2143 (tmtt) outliers start: 135 outliers final: 101 residues processed: 301 average time/residue: 0.4406 time to fit residues: 220.7151 Evaluate side-chains 288 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 171 time to evaluate : 3.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 102 THR Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain Y residue 117 MET Chi-restraints excluded: chain Y residue 141 LEU Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 198 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 9.9990 chunk 396 optimal weight: 20.0000 chunk 361 optimal weight: 50.0000 chunk 385 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 167 optimal weight: 0.5980 chunk 302 optimal weight: 0.8980 chunk 118 optimal weight: 0.0040 chunk 348 optimal weight: 5.9990 chunk 364 optimal weight: 8.9990 chunk 383 optimal weight: 7.9990 overall best weight: 2.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 31 HIS Y 3 GLN E 31 HIS ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 34641 Z= 0.278 Angle : 0.649 10.696 47148 Z= 0.330 Chirality : 0.047 0.271 5433 Planarity : 0.005 0.063 6072 Dihedral : 7.808 104.719 5198 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.73 % Allowed : 19.52 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.12), residues: 4266 helix: 1.00 (0.20), residues: 657 sheet: -0.83 (0.15), residues: 1209 loop : -2.22 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 353 HIS 0.008 0.001 HIS E 31 PHE 0.039 0.002 PHE H 29 TYR 0.021 0.001 TYR C1067 ARG 0.011 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 170 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6820 (ttt180) REVERT: B 425 LEU cc_start: 0.1174 (OUTLIER) cc_final: 0.0760 (tp) REVERT: B 719 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8504 (m) REVERT: B 901 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: B 977 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7821 (pp) REVERT: B 1031 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: B 1119 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8370 (p0) REVERT: A 392 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6372 (m-80) REVERT: A 697 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.7165 (ttp) REVERT: A 708 SER cc_start: 0.8087 (OUTLIER) cc_final: 0.7647 (m) REVERT: C 200 TYR cc_start: 0.6646 (OUTLIER) cc_final: 0.6170 (t80) REVERT: C 497 PHE cc_start: 0.5102 (OUTLIER) cc_final: 0.4555 (m-10) REVERT: C 954 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7133 (mt0) REVERT: C 962 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8778 (tt) REVERT: C 1107 ARG cc_start: 0.7917 (ttm170) cc_final: 0.7580 (mtt90) REVERT: H 72 ARG cc_start: 0.5081 (ttt180) cc_final: 0.4792 (ttt-90) REVERT: H 134 LYS cc_start: 0.2093 (ptmm) cc_final: 0.0545 (ptpt) REVERT: H 160 LYS cc_start: 0.3003 (mttm) cc_final: 0.1859 (pttm) REVERT: X 4 MET cc_start: 0.3971 (tmm) cc_final: 0.3685 (tmm) REVERT: Y 101 GLU cc_start: 0.5438 (OUTLIER) cc_final: 0.4451 (mp0) REVERT: Y 120 TRP cc_start: 0.5410 (OUTLIER) cc_final: 0.5189 (m-90) REVERT: E 21 ILE cc_start: 0.3335 (OUTLIER) cc_final: 0.2627 (mm) REVERT: E 35 TYR cc_start: 0.2776 (OUTLIER) cc_final: 0.1965 (t80) REVERT: E 174 LYS cc_start: 0.3231 (mttt) cc_final: 0.2212 (pttt) REVERT: F 43 LYS cc_start: 0.3451 (mmtm) cc_final: 0.2150 (tmtt) REVERT: F 69 THR cc_start: 0.0320 (OUTLIER) cc_final: -0.0060 (m) outliers start: 140 outliers final: 110 residues processed: 298 average time/residue: 0.4550 time to fit residues: 224.6042 Evaluate side-chains 294 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 165 time to evaluate : 3.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 102 THR Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 96 CYS Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain Y residue 120 TRP Chi-restraints excluded: chain Y residue 141 LEU Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 198 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 5.9990 chunk 407 optimal weight: 30.0000 chunk 248 optimal weight: 4.9990 chunk 193 optimal weight: 0.5980 chunk 283 optimal weight: 6.9990 chunk 427 optimal weight: 8.9990 chunk 393 optimal weight: 40.0000 chunk 340 optimal weight: 20.0000 chunk 35 optimal weight: 40.0000 chunk 262 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 34641 Z= 0.347 Angle : 0.689 10.934 47148 Z= 0.351 Chirality : 0.048 0.307 5433 Planarity : 0.005 0.063 6072 Dihedral : 7.783 105.535 5198 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.70 % Allowed : 19.54 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -2.01 (0.12), residues: 4266 helix: 0.79 (0.20), residues: 663 sheet: -0.88 (0.14), residues: 1214 loop : -2.29 (0.12), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 64 HIS 0.007 0.001 HIS E 31 PHE 0.031 0.002 PHE H 29 TYR 0.024 0.002 TYR B 170 ARG 0.014 0.001 ARG L 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 162 time to evaluate : 3.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6829 (ttt180) REVERT: B 425 LEU cc_start: 0.0698 (OUTLIER) cc_final: 0.0303 (tp) REVERT: B 719 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8554 (m) REVERT: B 901 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: B 977 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7844 (pp) REVERT: B 1031 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: B 1119 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8451 (p0) REVERT: A 392 PHE cc_start: 0.6969 (OUTLIER) cc_final: 0.6380 (m-80) REVERT: C 200 TYR cc_start: 0.6703 (OUTLIER) cc_final: 0.6240 (t80) REVERT: C 497 PHE cc_start: 0.5120 (OUTLIER) cc_final: 0.4583 (m-10) REVERT: C 900 MET cc_start: 0.7937 (mtm) cc_final: 0.7708 (mtp) REVERT: C 954 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.7169 (mt0) REVERT: C 1107 ARG cc_start: 0.7928 (ttm170) cc_final: 0.7656 (mtt90) REVERT: H 134 LYS cc_start: 0.2330 (ptmm) cc_final: 0.0786 (ptpt) REVERT: H 160 LYS cc_start: 0.3089 (mttm) cc_final: 0.1816 (pttm) REVERT: Y 101 GLU cc_start: 0.5477 (OUTLIER) cc_final: 0.4442 (mp0) REVERT: Y 117 MET cc_start: 0.4630 (OUTLIER) cc_final: 0.4065 (mmt) REVERT: Y 120 TRP cc_start: 0.5395 (OUTLIER) cc_final: 0.5054 (m-90) REVERT: E 21 ILE cc_start: 0.3363 (OUTLIER) cc_final: 0.2633 (mm) REVERT: E 35 TYR cc_start: 0.2818 (OUTLIER) cc_final: 0.2034 (t80) REVERT: E 174 LYS cc_start: 0.3249 (mttt) cc_final: 0.2223 (pttt) REVERT: F 43 LYS cc_start: 0.3250 (mmtm) cc_final: 0.1961 (tmtt) REVERT: F 69 THR cc_start: 0.0302 (OUTLIER) cc_final: -0.0030 (m) outliers start: 139 outliers final: 113 residues processed: 290 average time/residue: 0.4292 time to fit residues: 208.9258 Evaluate side-chains 287 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 157 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 102 THR Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 96 CYS Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain Y residue 117 MET Chi-restraints excluded: chain Y residue 120 TRP Chi-restraints excluded: chain Y residue 141 LEU Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 198 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 0.4980 chunk 362 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 340 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 350 optimal weight: 30.0000 chunk 43 optimal weight: 30.0000 chunk 62 optimal weight: 8.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A1142 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.180927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.152370 restraints weight = 65196.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.146429 restraints weight = 100249.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.143726 restraints weight = 87411.291| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.175 34641 Z= 0.564 Angle : 0.810 11.197 47148 Z= 0.417 Chirality : 0.053 0.352 5433 Planarity : 0.006 0.081 6072 Dihedral : 8.149 106.767 5198 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 3.83 % Allowed : 19.73 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -2.33 (0.12), residues: 4266 helix: 0.28 (0.19), residues: 659 sheet: -1.07 (0.14), residues: 1210 loop : -2.43 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 64 HIS 0.007 0.001 HIS E 31 PHE 0.044 0.003 PHE B1121 TYR 0.038 0.002 TYR B 170 ARG 0.023 0.001 ARG C 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5682.73 seconds wall clock time: 106 minutes 18.76 seconds (6378.76 seconds total)