Starting phenix.real_space_refine on Sat Apr 13 18:07:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knb_22941/04_2024/7knb_22941.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knb_22941/04_2024/7knb_22941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knb_22941/04_2024/7knb_22941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knb_22941/04_2024/7knb_22941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knb_22941/04_2024/7knb_22941.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knb_22941/04_2024/7knb_22941.pdb" } resolution = 3.93 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= 0.002 sd= 0.012 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 136 5.16 5 C 18616 2.51 5 N 4781 2.21 5 O 5691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 206": "OD1" <-> "OD2" Residue "D TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D ASP 216": "OD1" <-> "OD2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29224 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 7788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7788 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 49, 'TRANS': 956} Chain breaks: 8 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "A" Number of atoms: 7772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7772 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 49, 'TRANS': 956} Chain breaks: 8 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 8018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8018 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 51, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 15.22, per 1000 atoms: 0.52 Number of scatterers: 29224 At special positions: 0 Unit cell: (134.366, 152.352, 224.296, 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 136 16.00 O 5691 8.00 N 4781 7.00 C 18616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.07 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 234 " " NAG A1311 " - " ASN A 603 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 657 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B1134 " " NAG B1303 " - " ASN B1098 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 61 " " NAG B1311 " - " ASN B 234 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 343 " " NAG B1314 " - " ASN B 603 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C1134 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 234 " " NAG C1311 " - " ASN C 603 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 657 " " NAG D 701 " - " ASN D 546 " " NAG D 702 " - " ASN D 322 " " NAG D 703 " - " ASN D 432 " " NAG D 704 " - " ASN D 103 " " NAG D 705 " - " ASN D 90 " " NAG D 706 " - " ASN D 53 " " NAG E 1 " - " ASN C 717 " " NAG F 1 " - " ASN C 343 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 343 " " NAG I 1 " - " ASN B 717 " Time building additional restraints: 12.26 Conformation dependent library (CDL) restraints added in 5.3 seconds 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6832 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 43 sheets defined 31.2% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.605A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 4.023A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.516A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.994A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.662A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.762A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 762 Processing helix chain 'C' and resid 763 through 782 removed outlier: 3.624A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 777 " --> pdb=" O GLU C 773 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.612A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.044A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.545A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.330A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.217A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.696A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1120 Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.237A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.991A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 344 removed outlier: 4.250A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.695A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.288A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.867A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.892A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.742A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.885A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.947A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.663A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 942 removed outlier: 3.553A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.238A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.828A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.843A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.514A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.794A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 738 through 743 removed outlier: 3.514A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.587A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.544A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 772 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.717A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.710A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.724A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.287A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.646A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 965 removed outlier: 4.023A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN B 953 " --> pdb=" O GLN B 949 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (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: 3.657A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.678A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 4.399A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 51 removed outlier: 3.686A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 removed outlier: 3.896A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 91 through 101 removed outlier: 3.670A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 128 removed outlier: 4.565A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 removed outlier: 4.077A pdb=" N ASN D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.711A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.592A pdb=" N GLN D 175 " --> pdb=" O VAL D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 176 through 187 removed outlier: 3.665A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 194 removed outlier: 4.468A pdb=" N ARG D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.512A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 245 removed outlier: 3.950A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.662A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 267 removed outlier: 3.769A pdb=" N LEU D 266 " --> pdb=" O PRO D 263 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU D 267 " --> pdb=" O ALA D 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 263 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.806A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.658A pdb=" N GLU D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 removed outlier: 4.490A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 324 through 329' Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.508A pdb=" N MET D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET D 383 " --> pdb=" O ILE D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 4.099A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.639A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 447 removed outlier: 4.080A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.352A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 463 " --> pdb=" O TRP D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.658A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 511 through 514 removed outlier: 3.874A pdb=" N ARG D 514 " --> pdb=" O SER D 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 511 through 514' Processing helix chain 'D' and resid 515 through 523 removed outlier: 3.866A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 533 Processing helix chain 'D' and resid 547 through 559 Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.754A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 586 removed outlier: 4.046A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN D 586 " --> pdb=" O ARG D 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 581 through 586' Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.771A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.080A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 51 removed outlier: 4.380A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 103 through 106 removed outlier: 3.565A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.510A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 326 through 328 removed outlier: 3.741A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 43 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 376 through 380 removed outlier: 3.596A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.399A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 703 through 704 removed outlier: 6.772A pdb=" N ASN C 703 " --> pdb=" O LYS A 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.526A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1047 through 1051 removed outlier: 7.044A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N HIS C1101 " --> pdb=" O ASN C1098 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.079A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 787 through 789 removed outlier: 5.640A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 1086 through 1088 removed outlier: 3.512A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.605A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.605A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 49 through 51 removed outlier: 4.277A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 105 through 106 Processing sheet with id=AC1, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.085A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 323 through 328 removed outlier: 4.852A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 378 through 380 removed outlier: 3.854A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AC5, first strand: chain 'A' and resid 653 through 655 Processing sheet with id=AC6, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AC7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.698A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.698A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.279A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1086 through 1088 removed outlier: 3.720A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.785A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.539A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.564A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.860A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.871A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'B' and resid 539 through 542 Processing sheet with id=AD9, first strand: chain 'B' and resid 565 through 567 Processing sheet with id=AE1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.536A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.826A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.826A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.308A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE7, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.509A pdb=" N LEU D 359 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1007 hydrogen bonds defined for protein. 2802 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: 12.85 Time building geometry restraints manager: 13.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9292 1.34 - 1.47: 7464 1.47 - 1.59: 12950 1.59 - 1.72: 0 1.72 - 1.84: 183 Bond restraints: 29889 Sorted by residual: bond pdb=" N ASP A 994 " pdb=" CA ASP A 994 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.35e+00 bond pdb=" N LEU A 752 " pdb=" CA LEU A 752 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.61e+00 bond pdb=" N SER A 940 " pdb=" CA SER A 940 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.27e-02 6.20e+03 5.55e+00 bond pdb=" N THR A 941 " pdb=" CA THR A 941 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.34e+00 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.25e+00 ... (remaining 29884 not shown) Histogram of bond angle deviations from ideal: 98.94 - 105.95: 619 105.95 - 112.96: 16204 112.96 - 119.98: 10114 119.98 - 126.99: 13418 126.99 - 134.00: 316 Bond angle restraints: 40671 Sorted by residual: angle pdb=" CA TYR A 756 " pdb=" C TYR A 756 " pdb=" O TYR A 756 " ideal model delta sigma weight residual 120.55 116.48 4.07 1.06e+00 8.90e-01 1.47e+01 angle pdb=" CA THR A 941 " pdb=" C THR A 941 " pdb=" O THR A 941 " ideal model delta sigma weight residual 120.82 116.86 3.96 1.05e+00 9.07e-01 1.43e+01 angle pdb=" C TYR A 756 " pdb=" CA TYR A 756 " pdb=" CB TYR A 756 " ideal model delta sigma weight residual 110.79 116.71 -5.92 1.66e+00 3.63e-01 1.27e+01 angle pdb=" N ALA A 944 " pdb=" CA ALA A 944 " pdb=" C ALA A 944 " ideal model delta sigma weight residual 113.16 108.82 4.34 1.24e+00 6.50e-01 1.22e+01 angle pdb=" CA SER A 943 " pdb=" C SER A 943 " pdb=" O SER A 943 " ideal model delta sigma weight residual 121.54 117.71 3.83 1.16e+00 7.43e-01 1.09e+01 ... (remaining 40666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16699 17.93 - 35.86: 1434 35.86 - 53.78: 272 53.78 - 71.71: 74 71.71 - 89.64: 29 Dihedral angle restraints: 18508 sinusoidal: 7910 harmonic: 10598 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 22.47 70.53 1 1.00e+01 1.00e-02 6.40e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -150.26 64.26 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 151.36 -58.36 1 1.00e+01 1.00e-02 4.56e+01 ... (remaining 18505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4109 0.061 - 0.123: 594 0.123 - 0.184: 38 0.184 - 0.246: 2 0.246 - 0.307: 5 Chirality restraints: 4748 Sorted by residual: chirality pdb=" C1 NAG D 703 " pdb=" ND2 ASN D 432 " pdb=" C2 NAG D 703 " pdb=" O5 NAG D 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C1 NAG B1312 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1312 " pdb=" O5 NAG B1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 4745 not shown) Planarity restraints: 5244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " -0.049 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO B 337 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.036 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO C 987 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 271 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO A 272 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " 0.030 5.00e-02 4.00e+02 ... (remaining 5241 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2951 2.75 - 3.28: 30328 3.28 - 3.82: 47286 3.82 - 4.36: 55587 4.36 - 4.90: 93773 Nonbonded interactions: 229925 Sorted by model distance: nonbonded pdb=" OH TYR B 369 " pdb=" O PRO B 384 " model vdw 2.207 2.440 nonbonded pdb=" OG SER A 659 " pdb=" O THR A 696 " model vdw 2.213 2.440 nonbonded pdb=" N LYS C 187 " pdb=" O ILE C 210 " model vdw 2.220 2.520 nonbonded pdb=" OD1 ASP D 67 " pdb=" N LYS D 68 " model vdw 2.227 2.520 nonbonded pdb=" OG SER B 929 " pdb=" NZ LYS B 933 " model vdw 2.227 2.520 ... (remaining 229920 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 66 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 189 or (resid 190 and (name N or n \ ame CA or name C or name O or name CB )) or resid 191 through 289 or (resid 290 \ and (name N or name CA or name C or name O or name CB )) or resid 291 through 62 \ 0 or resid 640 through 676 or resid 690 through 1146 or resid 1301 through 1313) \ ) selection = (chain 'B' and (resid 26 through 66 or resid 81 through 95 or (resid 96 through \ 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (resi \ d 99 through 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) or \ resid 103 through 139 or (resid 140 through 141 and (name N or name CA or name \ C or name O or name CB )) or (resid 156 and (name N or name CA or name C or name \ O or name CB )) or resid 157 through 158 or (resid 159 through 160 and (name N \ or name CA or name C or name O or name CB )) or resid 161 through 172 or (resid \ 173 and (name N or name CA or name C or name O or name CB )) or resid 174 throug \ h 176 or (resid 187 through 188 and (name N or name CA or name C or name O or na \ me CB )) or resid 189 through 194 or (resid 195 through 198 and (name N or name \ CA or name C or name O or name CB )) or resid 199 or (resid 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 243 or resid 264 t \ hrough 280 or (resid 281 and (name N or name CA or name C or name O or name CB ) \ ) or resid 282 through 620 or resid 640 through 811 or resid 815 through 828 or \ resid 853 through 1146 or resid 1302 through 1314)) selection = (chain 'C' and (resid 26 through 66 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 101 or (resid 102 and (name N or n \ ame CA or name C or name O or name CB )) or resid 103 through 114 or (resid 115 \ and (name N or name CA or name C or name O or name CB )) or resid 116 through 13 \ 4 or (resid 135 and (name N or name CA or name C or name O or name CB )) or resi \ d 136 through 189 or (resid 190 and (name N or name CA or name C or name O or na \ me CB )) or resid 191 through 289 or (resid 290 and (name N or name CA or name C \ or name O or name CB )) or resid 291 through 620 or resid 640 through 676 or re \ sid 690 through 1146 or resid 1301 through 1313)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 16.730 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 79.730 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.220 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29889 Z= 0.209 Angle : 0.551 7.386 40671 Z= 0.290 Chirality : 0.044 0.307 4748 Planarity : 0.003 0.074 5193 Dihedral : 13.766 89.639 11550 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3583 helix: -0.03 (0.18), residues: 894 sheet: 0.11 (0.22), residues: 617 loop : -0.69 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 271 HIS 0.006 0.000 HIS D 540 PHE 0.007 0.001 PHE B 338 TYR 0.026 0.001 TYR D 217 ARG 0.010 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8900 (mpp) cc_final: 0.8616 (mpp) REVERT: A 1050 MET cc_start: 0.8677 (pmm) cc_final: 0.8359 (pmm) REVERT: B 731 MET cc_start: 0.8142 (ptm) cc_final: 0.7801 (ptm) REVERT: B 1050 MET cc_start: 0.8877 (pmm) cc_final: 0.8393 (pmm) REVERT: D 270 MET cc_start: 0.5474 (tmm) cc_final: 0.4634 (tmm) REVERT: D 480 MET cc_start: -0.1050 (ppp) cc_final: -0.1273 (ppp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.3942 time to fit residues: 59.7926 Evaluate side-chains 71 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 chunk 282 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 chunk 327 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN C 87 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 955 ASN C1083 HIS A 450 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A1071 GLN A1083 HIS B 450 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN D 42 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 29889 Z= 0.406 Angle : 0.715 10.502 40671 Z= 0.374 Chirality : 0.047 0.394 4748 Planarity : 0.005 0.048 5193 Dihedral : 7.103 59.709 5058 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.38 % Allowed : 6.88 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3583 helix: 0.13 (0.17), residues: 963 sheet: -0.32 (0.22), residues: 584 loop : -0.88 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 64 HIS 0.009 0.002 HIS B 207 PHE 0.018 0.002 PHE C 392 TYR 0.028 0.002 TYR C 756 ARG 0.008 0.001 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 3.463 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.8930 (mpp) cc_final: 0.8606 (mmm) REVERT: A 985 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8212 (p0) REVERT: B 517 LEU cc_start: 0.7319 (tp) cc_final: 0.6231 (tp) REVERT: B 697 MET cc_start: 0.8976 (mmm) cc_final: 0.8506 (mmp) REVERT: B 731 MET cc_start: 0.8303 (ptm) cc_final: 0.7909 (ptm) REVERT: B 900 MET cc_start: 0.8659 (pmm) cc_final: 0.8441 (pmm) REVERT: B 1050 MET cc_start: 0.9208 (pmm) cc_final: 0.8671 (pmm) REVERT: D 270 MET cc_start: 0.5486 (tmm) cc_final: 0.4847 (tmm) REVERT: D 383 MET cc_start: 0.7960 (mpp) cc_final: 0.7597 (pmm) REVERT: D 480 MET cc_start: -0.0173 (ppp) cc_final: -0.0427 (ppp) outliers start: 12 outliers final: 7 residues processed: 87 average time/residue: 0.3740 time to fit residues: 58.6551 Evaluate side-chains 79 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain D residue 159 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 328 optimal weight: 7.9990 chunk 354 optimal weight: 6.9990 chunk 292 optimal weight: 5.9990 chunk 325 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 263 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN A 388 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29889 Z= 0.151 Angle : 0.498 9.234 40671 Z= 0.256 Chirality : 0.044 0.353 4748 Planarity : 0.004 0.055 5193 Dihedral : 6.378 59.451 5058 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.67 % Allowed : 8.83 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3583 helix: 0.60 (0.17), residues: 981 sheet: -0.37 (0.21), residues: 605 loop : -0.73 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 168 HIS 0.004 0.001 HIS D 417 PHE 0.015 0.001 PHE B 392 TYR 0.012 0.001 TYR B1067 ARG 0.005 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 3.532 Fit side-chains REVERT: C 1050 MET cc_start: 0.9263 (pmm) cc_final: 0.8961 (pmm) REVERT: A 388 ASN cc_start: 0.7236 (OUTLIER) cc_final: 0.7010 (p0) REVERT: A 900 MET cc_start: 0.8914 (mpp) cc_final: 0.8478 (mmm) REVERT: B 697 MET cc_start: 0.8897 (mmm) cc_final: 0.8541 (mmp) REVERT: B 1050 MET cc_start: 0.9023 (pmm) cc_final: 0.8491 (pmm) REVERT: D 270 MET cc_start: 0.5350 (tmm) cc_final: 0.4931 (tmm) REVERT: D 480 MET cc_start: -0.0354 (ppp) cc_final: -0.0634 (ppp) outliers start: 21 outliers final: 10 residues processed: 95 average time/residue: 0.3642 time to fit residues: 61.7541 Evaluate side-chains 82 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain D residue 159 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 30.0000 chunk 246 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 329 optimal weight: 10.0000 chunk 348 optimal weight: 8.9990 chunk 172 optimal weight: 0.0470 chunk 312 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 935 GLN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29889 Z= 0.215 Angle : 0.519 9.403 40671 Z= 0.268 Chirality : 0.043 0.357 4748 Planarity : 0.004 0.055 5193 Dihedral : 5.981 58.101 5058 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.21 % Allowed : 10.52 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3583 helix: 0.74 (0.17), residues: 989 sheet: -0.38 (0.21), residues: 588 loop : -0.78 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.005 0.001 HIS C1088 PHE 0.012 0.001 PHE B 329 TYR 0.011 0.001 TYR A 269 ARG 0.009 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 70 time to evaluate : 3.470 Fit side-chains REVERT: C 1050 MET cc_start: 0.9125 (pmm) cc_final: 0.8776 (pmm) REVERT: A 388 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7468 (p0) REVERT: A 900 MET cc_start: 0.9010 (mpp) cc_final: 0.8315 (mmp) REVERT: A 985 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8127 (p0) REVERT: A 1050 MET cc_start: 0.8464 (pmm) cc_final: 0.8173 (mpp) REVERT: B 697 MET cc_start: 0.9012 (mmm) cc_final: 0.8677 (mmp) REVERT: B 900 MET cc_start: 0.8777 (pmm) cc_final: 0.8332 (pmm) REVERT: B 1050 MET cc_start: 0.9006 (pmm) cc_final: 0.8364 (pmm) REVERT: D 157 ASP cc_start: 0.5591 (OUTLIER) cc_final: 0.5385 (p0) REVERT: D 270 MET cc_start: 0.5391 (tmm) cc_final: 0.4844 (tmm) REVERT: D 480 MET cc_start: -0.0387 (ppp) cc_final: -0.0639 (ppp) outliers start: 38 outliers final: 21 residues processed: 106 average time/residue: 0.3749 time to fit residues: 70.8395 Evaluate side-chains 91 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 67 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 463 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 7.9990 chunk 198 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 297 optimal weight: 0.8980 chunk 241 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 313 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 965 GLN C1036 GLN A 81 ASN A 239 GLN A 388 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 29889 Z= 0.312 Angle : 0.607 11.029 40671 Z= 0.312 Chirality : 0.045 0.354 4748 Planarity : 0.004 0.057 5193 Dihedral : 6.064 59.121 5058 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.07 % Allowed : 11.85 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3583 helix: 0.65 (0.17), residues: 996 sheet: -0.56 (0.20), residues: 585 loop : -0.88 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 64 HIS 0.007 0.001 HIS C 655 PHE 0.017 0.002 PHE C 168 TYR 0.015 0.002 TYR A 269 ARG 0.007 0.001 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 73 time to evaluate : 4.656 Fit side-chains REVERT: A 731 MET cc_start: 0.8591 (ppp) cc_final: 0.8126 (ppp) REVERT: A 900 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8493 (mmt) REVERT: A 985 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8230 (p0) REVERT: B 697 MET cc_start: 0.9048 (mmm) cc_final: 0.8496 (mmp) REVERT: B 740 MET cc_start: 0.7279 (ppp) cc_final: 0.6973 (ppp) REVERT: B 900 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8512 (pmm) REVERT: B 1050 MET cc_start: 0.9086 (pmm) cc_final: 0.8404 (pmm) REVERT: D 270 MET cc_start: 0.5644 (tmm) cc_final: 0.5236 (tmm) REVERT: D 480 MET cc_start: -0.0410 (ppp) cc_final: -0.0618 (ppp) outliers start: 65 outliers final: 36 residues processed: 131 average time/residue: 0.3825 time to fit residues: 89.7994 Evaluate side-chains 107 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 68 time to evaluate : 3.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 463 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 9.9990 chunk 314 optimal weight: 0.7980 chunk 68 optimal weight: 0.0070 chunk 204 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 349 optimal weight: 4.9990 chunk 289 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29889 Z= 0.137 Angle : 0.509 9.504 40671 Z= 0.258 Chirality : 0.044 0.342 4748 Planarity : 0.003 0.059 5193 Dihedral : 5.640 57.973 5058 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.40 % Allowed : 13.26 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3583 helix: 0.88 (0.17), residues: 998 sheet: -0.48 (0.21), residues: 579 loop : -0.84 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 168 HIS 0.003 0.001 HIS D 417 PHE 0.011 0.001 PHE B 329 TYR 0.013 0.001 TYR B1067 ARG 0.004 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 73 time to evaluate : 3.758 Fit side-chains revert: symmetry clash REVERT: C 916 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8955 (tp) REVERT: C 1050 MET cc_start: 0.9112 (pmm) cc_final: 0.8610 (pmm) REVERT: A 985 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8209 (p0) REVERT: A 1050 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8196 (mpp) REVERT: B 210 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8277 (tp) REVERT: B 740 MET cc_start: 0.7065 (ppp) cc_final: 0.6773 (ppp) REVERT: B 1050 MET cc_start: 0.8911 (pmm) cc_final: 0.8342 (pmm) REVERT: D 270 MET cc_start: 0.5522 (tmm) cc_final: 0.5056 (tmm) outliers start: 44 outliers final: 22 residues processed: 113 average time/residue: 0.3861 time to fit residues: 76.8054 Evaluate side-chains 97 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 71 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain D residue 463 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 255 optimal weight: 0.2980 chunk 197 optimal weight: 0.7980 chunk 294 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 347 optimal weight: 10.0000 chunk 217 optimal weight: 0.6980 chunk 212 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29889 Z= 0.149 Angle : 0.506 9.510 40671 Z= 0.254 Chirality : 0.043 0.343 4748 Planarity : 0.003 0.058 5193 Dihedral : 5.439 58.028 5058 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.34 % Allowed : 14.15 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3583 helix: 0.97 (0.17), residues: 997 sheet: -0.46 (0.21), residues: 581 loop : -0.79 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 168 HIS 0.003 0.001 HIS D 417 PHE 0.019 0.001 PHE B 392 TYR 0.012 0.001 TYR B1067 ARG 0.005 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 73 time to evaluate : 3.451 Fit side-chains REVERT: C 1050 MET cc_start: 0.9177 (pmm) cc_final: 0.8701 (pmm) REVERT: A 900 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8743 (mpp) REVERT: A 985 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8230 (p0) REVERT: A 1050 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8124 (mpp) REVERT: B 697 MET cc_start: 0.8849 (mmm) cc_final: 0.8132 (mmm) REVERT: B 740 MET cc_start: 0.7053 (ppp) cc_final: 0.6758 (ppp) REVERT: B 1050 MET cc_start: 0.8884 (pmm) cc_final: 0.8211 (pmm) REVERT: D 270 MET cc_start: 0.5571 (tmm) cc_final: 0.5056 (tmm) outliers start: 42 outliers final: 29 residues processed: 111 average time/residue: 0.3806 time to fit residues: 74.9809 Evaluate side-chains 102 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 70 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain D residue 463 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 237 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29889 Z= 0.182 Angle : 0.520 9.458 40671 Z= 0.263 Chirality : 0.043 0.345 4748 Planarity : 0.003 0.057 5193 Dihedral : 5.383 58.042 5058 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.34 % Allowed : 14.53 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3583 helix: 1.02 (0.18), residues: 994 sheet: -0.45 (0.20), residues: 605 loop : -0.81 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 168 HIS 0.003 0.001 HIS C 655 PHE 0.024 0.001 PHE A 306 TYR 0.018 0.001 TYR A 473 ARG 0.005 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 70 time to evaluate : 3.543 Fit side-chains REVERT: A 731 MET cc_start: 0.8455 (ppp) cc_final: 0.8041 (ppp) REVERT: A 740 MET cc_start: 0.8485 (tpp) cc_final: 0.8188 (mtt) REVERT: A 900 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8752 (mpp) REVERT: A 985 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8257 (p0) REVERT: A 1050 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8126 (mpp) REVERT: B 210 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8294 (tp) REVERT: B 697 MET cc_start: 0.8854 (mmm) cc_final: 0.8189 (mmm) REVERT: B 740 MET cc_start: 0.7078 (ppp) cc_final: 0.6835 (ppp) REVERT: B 1050 MET cc_start: 0.8918 (pmm) cc_final: 0.8339 (pmm) REVERT: D 270 MET cc_start: 0.5406 (tmm) cc_final: 0.4892 (tmm) outliers start: 42 outliers final: 34 residues processed: 109 average time/residue: 0.3723 time to fit residues: 72.7124 Evaluate side-chains 105 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 67 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 463 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 20.0000 chunk 333 optimal weight: 0.3980 chunk 304 optimal weight: 8.9990 chunk 324 optimal weight: 30.0000 chunk 195 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 254 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 292 optimal weight: 7.9990 chunk 306 optimal weight: 6.9990 chunk 323 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29889 Z= 0.159 Angle : 0.515 10.590 40671 Z= 0.258 Chirality : 0.044 0.341 4748 Planarity : 0.003 0.058 5193 Dihedral : 5.315 58.122 5058 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.31 % Allowed : 14.69 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3583 helix: 1.08 (0.18), residues: 993 sheet: -0.47 (0.20), residues: 605 loop : -0.82 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 168 HIS 0.002 0.001 HIS C 655 PHE 0.021 0.001 PHE B 392 TYR 0.012 0.001 TYR B1067 ARG 0.005 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 68 time to evaluate : 3.412 Fit side-chains REVERT: C 1050 MET cc_start: 0.9137 (pmm) cc_final: 0.8789 (pmm) REVERT: A 731 MET cc_start: 0.8473 (ppp) cc_final: 0.7975 (ppp) REVERT: A 740 MET cc_start: 0.8501 (tpp) cc_final: 0.8188 (mtt) REVERT: A 900 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8768 (mpp) REVERT: A 985 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8242 (p0) REVERT: A 1050 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8178 (mpp) REVERT: B 697 MET cc_start: 0.8782 (mmm) cc_final: 0.8143 (mmm) REVERT: B 740 MET cc_start: 0.7023 (ppp) cc_final: 0.6755 (ppp) REVERT: B 1050 MET cc_start: 0.8877 (pmm) cc_final: 0.8269 (pmm) REVERT: D 152 MET cc_start: -0.5878 (tpp) cc_final: -0.6103 (tmm) REVERT: D 270 MET cc_start: 0.5528 (tmm) cc_final: 0.5065 (tmm) outliers start: 41 outliers final: 34 residues processed: 106 average time/residue: 0.3841 time to fit residues: 72.5631 Evaluate side-chains 103 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 66 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 463 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 4.9990 chunk 342 optimal weight: 8.9990 chunk 209 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 238 optimal weight: 30.0000 chunk 359 optimal weight: 10.0000 chunk 331 optimal weight: 5.9990 chunk 286 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 29889 Z= 0.255 Angle : 0.579 11.157 40671 Z= 0.293 Chirality : 0.044 0.345 4748 Planarity : 0.004 0.056 5193 Dihedral : 5.560 58.990 5058 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.31 % Allowed : 14.85 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3583 helix: 0.99 (0.18), residues: 995 sheet: -0.59 (0.20), residues: 609 loop : -0.84 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 64 HIS 0.006 0.001 HIS C 655 PHE 0.025 0.001 PHE A 306 TYR 0.014 0.001 TYR A 269 ARG 0.025 0.001 ARG A 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 66 time to evaluate : 3.580 Fit side-chains REVERT: C 1050 MET cc_start: 0.9141 (pmm) cc_final: 0.8747 (pmm) REVERT: A 740 MET cc_start: 0.8532 (tpp) cc_final: 0.7991 (tpp) REVERT: A 882 ILE cc_start: 0.9583 (OUTLIER) cc_final: 0.9289 (tp) REVERT: A 900 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8433 (mmt) REVERT: A 985 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8317 (p0) REVERT: A 1050 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8130 (mpp) REVERT: B 210 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8392 (tp) REVERT: B 697 MET cc_start: 0.8917 (mmm) cc_final: 0.8380 (mmm) REVERT: B 740 MET cc_start: 0.7227 (ppp) cc_final: 0.6987 (ppp) REVERT: B 1050 MET cc_start: 0.8997 (pmm) cc_final: 0.8407 (pmm) REVERT: D 270 MET cc_start: 0.5534 (tmm) cc_final: 0.4996 (tmm) REVERT: D 323 MET cc_start: 0.3337 (tpp) cc_final: 0.3002 (tpp) outliers start: 41 outliers final: 33 residues processed: 103 average time/residue: 0.3757 time to fit residues: 69.5601 Evaluate side-chains 103 residues out of total 3187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 65 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 463 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 20.0000 chunk 305 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 264 optimal weight: 0.0570 chunk 42 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 286 optimal weight: 0.0060 chunk 120 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 36 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** 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 = 0.3630 r_free = 0.3630 target = 0.051153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.033401 restraints weight = 300443.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.033608 restraints weight = 163965.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.033990 restraints weight = 109550.486| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29889 Z= 0.129 Angle : 0.524 11.233 40671 Z= 0.261 Chirality : 0.044 0.335 4748 Planarity : 0.003 0.060 5193 Dihedral : 5.243 59.249 5058 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.12 % Allowed : 15.14 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3583 helix: 1.20 (0.18), residues: 986 sheet: -0.51 (0.20), residues: 613 loop : -0.86 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 168 HIS 0.003 0.001 HIS D 540 PHE 0.017 0.001 PHE D 603 TYR 0.013 0.001 TYR B1067 ARG 0.007 0.000 ARG A 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4564.78 seconds wall clock time: 86 minutes 27.58 seconds (5187.58 seconds total)