Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 20 15:01:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbh_32398/08_2023/7wbh_32398.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbh_32398/08_2023/7wbh_32398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbh_32398/08_2023/7wbh_32398.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbh_32398/08_2023/7wbh_32398.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbh_32398/08_2023/7wbh_32398.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbh_32398/08_2023/7wbh_32398.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 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 129 5.16 5 C 18573 2.51 5 N 4761 2.21 5 O 5724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 63": "OD1" <-> "OD2" Residue "U PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 103": "OD1" <-> "OD2" Residue "V TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 70": "OD1" <-> "OD2" Residue "Q TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 29187 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 7761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7761 Classifications: {'peptide': 1006} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 23} Link IDs: {'PTRANS': 54, 'TRANS': 951} Chain breaks: 8 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 7732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7732 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 54, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7677 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 54, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 82 Chain: "U" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "V" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "O" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "Q" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "P" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "S" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 chiralities: 6 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.85, per 1000 atoms: 0.47 Number of scatterers: 29187 At special positions: 0 Unit cell: (144.72, 166.32, 192.24, 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 129 16.00 O 5724 8.00 N 4761 7.00 C 18573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.03 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=2.02 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=2.06 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=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 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 U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1201 " - " ASN A 282 " " NAG A1202 " - " ASN A 603 " " NAG A1204 " - " ASN A 657 " " NAG A1205 " - " ASN A 709 " " NAG B1303 " - " ASN B 282 " " NAG B1306 " - " ASN B 616 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG D 1 " - " ASN A 343 " " NAG E 1 " - " ASN B 343 " " NAG F 1 " - " ASN C 343 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " Time building additional restraints: 11.35 Conformation dependent library (CDL) restraints added in 4.1 seconds 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6846 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 69 sheets defined 19.4% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.503A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.849A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.655A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.756A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.823A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.984A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.773A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.534A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.857A 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: 3.893A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.606A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.586A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.285A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.847A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.693A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.829A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.760A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.307A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.647A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.190A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.808A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.877A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.090A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.521A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.281A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.316A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.676A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.238A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.544A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.077A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 400 through 403 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.555A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.195A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.757A pdb=" N VAL A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 714 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.233A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.011A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.044A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.975A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.422A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.578A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.512A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.529A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.529A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.572A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 539 through 543 removed outlier: 4.952A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.115A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.637A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.088A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.504A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.327A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.327A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.876A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.114A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.681A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.405A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.729A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.886A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.167A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.230A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.025A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.630A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF6, first strand: chain 'U' and resid 5 through 6 removed outlier: 3.587A pdb=" N VAL U 5 " --> pdb=" O LYS U 23 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 11 through 12 removed outlier: 3.890A pdb=" N LYS U 12 " --> pdb=" O THR U 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'U' and resid 17 through 20 Processing sheet with id=AF9, first strand: chain 'U' and resid 58 through 60 removed outlier: 3.575A pdb=" N THR U 59 " --> pdb=" O TRP U 50 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP U 36 " --> pdb=" O MET U 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 5 through 7 removed outlier: 3.624A pdb=" N THR V 22 " --> pdb=" O SER V 7 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL V 19 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE V 21 " --> pdb=" O LEU V 73 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU V 73 " --> pdb=" O ILE V 21 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.929A pdb=" N LEU V 11 " --> pdb=" O LYS V 103 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU V 105 " --> pdb=" O LEU V 11 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE V 48 " --> pdb=" O TRP V 35 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN V 37 " --> pdb=" O LEU V 46 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU V 46 " --> pdb=" O GLN V 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 3 through 6 removed outlier: 3.713A pdb=" N GLN O 3 " --> pdb=" O SER O 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER O 25 " --> pdb=" O GLN O 3 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.942A pdb=" N LYS O 12 " --> pdb=" O THR O 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'O' and resid 17 through 20 removed outlier: 3.722A pdb=" N THR O 78 " --> pdb=" O ASP O 73 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 36 through 39 removed outlier: 7.003A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 93 through 94 removed outlier: 3.898A pdb=" N TYR O 94 " --> pdb=" O THR O 113 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR O 113 " --> pdb=" O TYR O 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'Q' and resid 5 through 7 removed outlier: 3.642A pdb=" N THR Q 22 " --> pdb=" O SER Q 7 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL Q 19 " --> pdb=" O ILE Q 75 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE Q 21 " --> pdb=" O LEU Q 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE Q 71 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP Q 70 " --> pdb=" O SER Q 67 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER Q 67 " --> pdb=" O ASP Q 70 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 10 through 13 removed outlier: 3.721A pdb=" N LEU Q 11 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU Q 105 " --> pdb=" O LEU Q 11 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 48 through 49 Processing sheet with id=AH2, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.761A pdb=" N GLN P 3 " --> pdb=" O SER P 25 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER P 25 " --> pdb=" O GLN P 3 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.943A pdb=" N LYS P 12 " --> pdb=" O THR P 116 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL P 115 " --> pdb=" O ALA P 92 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA P 92 " --> pdb=" O VAL P 115 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N MET P 34 " --> pdb=" O TRP P 50 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N TRP P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 18 through 20 removed outlier: 4.024A pdb=" N THR P 78 " --> pdb=" O ASP P 73 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP P 73 " --> pdb=" O THR P 78 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'S' and resid 4 through 5 removed outlier: 3.575A pdb=" N VAL S 19 " --> pdb=" O ILE S 75 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE S 21 " --> pdb=" O LEU S 73 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU S 73 " --> pdb=" O ILE S 21 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE S 71 " --> pdb=" O CYS S 23 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP S 70 " --> pdb=" O SER S 67 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'S' and resid 10 through 12 removed outlier: 7.006A pdb=" N LEU S 11 " --> pdb=" O GLU S 105 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN S 37 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU S 46 " --> pdb=" O GLN S 37 " (cutoff:3.500A) 1017 hydrogen bonds defined for protein. 2820 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: 13.36 Time building geometry restraints manager: 12.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9175 1.35 - 1.47: 7913 1.47 - 1.60: 12602 1.60 - 1.73: 0 1.73 - 1.86: 162 Bond restraints: 29852 Sorted by residual: bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C LEU B 560 " pdb=" N PRO B 561 " ideal model delta sigma weight residual 1.337 1.370 -0.034 9.80e-03 1.04e+04 1.17e+01 bond pdb=" C VAL C 83 " pdb=" N LEU C 84 " ideal model delta sigma weight residual 1.331 1.385 -0.054 1.59e-02 3.96e+03 1.14e+01 bond pdb=" C LEU A 560 " pdb=" N PRO A 561 " ideal model delta sigma weight residual 1.337 1.374 -0.037 1.11e-02 8.12e+03 1.12e+01 bond pdb=" C LYS B 462 " pdb=" N PRO B 463 " ideal model delta sigma weight residual 1.332 1.376 -0.044 1.34e-02 5.57e+03 1.10e+01 ... (remaining 29847 not shown) Histogram of bond angle deviations from ideal: 97.72 - 105.39: 650 105.39 - 113.07: 15642 113.07 - 120.75: 13193 120.75 - 128.42: 10979 128.42 - 136.10: 189 Bond angle restraints: 40653 Sorted by residual: angle pdb=" CA LYS C 378 " pdb=" CB LYS C 378 " pdb=" CG LYS C 378 " ideal model delta sigma weight residual 114.10 127.48 -13.38 2.00e+00 2.50e-01 4.48e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 118.48 -7.78 1.22e+00 6.72e-01 4.07e+01 angle pdb=" C PHE A 515 " pdb=" N GLU A 516 " pdb=" CA GLU A 516 " ideal model delta sigma weight residual 120.79 129.48 -8.69 1.39e+00 5.18e-01 3.91e+01 angle pdb=" C SER B 172 " pdb=" N GLN B 173 " pdb=" CA GLN B 173 " ideal model delta sigma weight residual 120.49 129.29 -8.80 1.42e+00 4.96e-01 3.84e+01 angle pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" C CYS B 525 " ideal model delta sigma weight residual 107.73 115.71 -7.98 1.34e+00 5.57e-01 3.55e+01 ... (remaining 40648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15662 17.95 - 35.90: 1263 35.90 - 53.85: 240 53.85 - 71.80: 56 71.80 - 89.75: 26 Dihedral angle restraints: 17247 sinusoidal: 6585 harmonic: 10662 Sorted by residual: dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual 93.00 177.74 -84.74 1 1.00e+01 1.00e-02 8.72e+01 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 19.04 73.96 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -156.50 70.50 1 1.00e+01 1.00e-02 6.40e+01 ... (remaining 17244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4385 0.114 - 0.228: 318 0.228 - 0.342: 30 0.342 - 0.456: 11 0.456 - 0.570: 4 Chirality restraints: 4748 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.13e+00 chirality pdb=" C2 NAG K 1 " pdb=" C1 NAG K 1 " pdb=" C3 NAG K 1 " pdb=" N2 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.02 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.50e+00 ... (remaining 4745 not shown) Planarity restraints: 5206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 282 " 0.007 2.00e-02 2.50e+03 4.32e-02 2.34e+01 pdb=" CG ASN A 282 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN A 282 " 0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN A 282 " -0.052 2.00e-02 2.50e+03 pdb=" C1 NAG A1201 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 38 " 0.073 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO A 39 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 38 " -0.064 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO C 39 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO C 39 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 39 " -0.053 5.00e-02 4.00e+02 ... (remaining 5203 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 8571 2.83 - 3.35: 23155 3.35 - 3.86: 48407 3.86 - 4.38: 51575 4.38 - 4.90: 92464 Nonbonded interactions: 224172 Sorted by model distance: nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.310 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.317 2.440 nonbonded pdb=" OH TYR B 741 " pdb=" O LEU B 962 " model vdw 2.325 2.440 nonbonded pdb=" OG SER B 349 " pdb=" O LEU B 452 " model vdw 2.329 2.440 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.329 2.440 ... (remaining 224167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 66 or resid 81 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 128 or ( \ resid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ through 140 or (resid 157 through 160 and (name N or name CA or name C or name O \ or name CB )) or resid 161 through 187 or (resid 188 and (name N or name CA or \ name C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA \ or name C or name O or name CB )) or resid 191 through 194 or (resid 195 throug \ h 198 and (name N or name CA or name C or name O or name CB )) or resid 199 thro \ ugh 209 or resid 217 through 236 or (resid 237 and (name N or name CA or name C \ or name O or name CB )) or resid 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 241 or resid 263 through 331 or \ (resid 332 through 333 and (name N or name CA or name C or name O or name CB )) \ or resid 334 through 620 or resid 641 through 1146 or resid 1201 through 1206)) \ selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 195 or (resid 196 through 19 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 199 through \ 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) or re \ sid 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) o \ r resid 240 through 289 or (resid 290 and (name N or name CA or name C or name O \ or name CB )) or resid 291 through 527 or (resid 528 through 529 and (name N or \ name CA or name C or name O or name CB )) or resid 530 through 620 or resid 641 \ through 1146 or resid 1301 through 1306)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 187 or (resid 188 and (name N or n \ ame CA or name C or name O or name CB )) or resid 189 through 209 or resid 217 t \ hrough 241 or resid 263 through 280 or (resid 281 and (name N or name CA or name \ C or name O or name CB )) or resid 282 through 1146 or resid 1301 through 1306) \ ) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'U' } ncs_group { reference = chain 'Q' selection = (chain 'S' and resid 1 through 107) selection = chain 'V' } 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: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 16.140 Check model and map are aligned: 0.470 Set scattering table: 0.300 Process input model: 74.780 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 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 : 0.006 0.101 29852 Z= 0.404 Angle : 1.130 19.142 40653 Z= 0.623 Chirality : 0.067 0.570 4748 Planarity : 0.009 0.112 5179 Dihedral : 13.923 89.749 10269 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.12), residues: 3615 helix: -2.12 (0.15), residues: 652 sheet: -1.00 (0.17), residues: 833 loop : -2.08 (0.12), residues: 2130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 317 time to evaluate : 3.893 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 318 average time/residue: 0.3635 time to fit residues: 195.2917 Evaluate side-chains 233 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.946 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 9.9990 chunk 275 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 185 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 284 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 329 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 134 GLN A 580 GLN A 926 GLN A1135 ASN B 448 ASN B 658 ASN B 755 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 914 ASN B 965 GLN B 969 ASN B1134 ASN C 417 ASN C 955 ASN V 27 GLN Q 92 ASN P 6 GLN P 82 GLN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 29852 Z= 0.265 Angle : 0.640 11.080 40653 Z= 0.327 Chirality : 0.047 0.462 4748 Planarity : 0.005 0.070 5179 Dihedral : 5.211 31.128 3928 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.18 % Favored : 95.80 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.13), residues: 3615 helix: -0.04 (0.20), residues: 655 sheet: -0.70 (0.17), residues: 867 loop : -1.76 (0.12), residues: 2093 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 250 time to evaluate : 3.186 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 275 average time/residue: 0.3851 time to fit residues: 177.0592 Evaluate side-chains 235 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 214 time to evaluate : 3.187 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3152 time to fit residues: 16.2273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 183 optimal weight: 0.0470 chunk 102 optimal weight: 10.0000 chunk 274 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 330 optimal weight: 6.9990 chunk 356 optimal weight: 9.9990 chunk 294 optimal weight: 0.8980 chunk 327 optimal weight: 5.9990 chunk 112 optimal weight: 0.0370 chunk 264 optimal weight: 2.9990 overall best weight: 0.9358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 448 ASN B 919 ASN B 955 ASN B1134 ASN C 414 GLN C 417 ASN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 29852 Z= 0.187 Angle : 0.582 9.616 40653 Z= 0.293 Chirality : 0.045 0.423 4748 Planarity : 0.004 0.059 5179 Dihedral : 4.821 30.946 3928 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.71 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 3615 helix: 0.72 (0.21), residues: 651 sheet: -0.58 (0.17), residues: 894 loop : -1.59 (0.13), residues: 2070 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 225 time to evaluate : 3.431 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 241 average time/residue: 0.3754 time to fit residues: 153.1693 Evaluate side-chains 211 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 201 time to evaluate : 3.154 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2871 time to fit residues: 9.8261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 326 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 171 optimal weight: 0.0050 chunk 36 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 331 optimal weight: 5.9990 chunk 350 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 314 optimal weight: 10.0000 chunk 94 optimal weight: 0.2980 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 394 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 641 ASN B 957 GLN B1002 GLN C 207 HIS U 82 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN S 37 GLN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 29852 Z= 0.205 Angle : 0.579 10.767 40653 Z= 0.289 Chirality : 0.046 0.528 4748 Planarity : 0.004 0.053 5179 Dihedral : 4.657 32.139 3928 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3615 helix: 1.08 (0.21), residues: 648 sheet: -0.61 (0.17), residues: 933 loop : -1.47 (0.13), residues: 2034 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 220 time to evaluate : 3.385 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 14 residues processed: 248 average time/residue: 0.3775 time to fit residues: 158.3621 Evaluate side-chains 209 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 195 time to evaluate : 3.096 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2640 time to fit residues: 11.5499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 292 optimal weight: 1.9990 chunk 199 optimal weight: 0.0040 chunk 5 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 299 optimal weight: 0.4980 chunk 242 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 314 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1135 ASN B 437 ASN B 448 ASN B 658 ASN B1005 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN P 35 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 29852 Z= 0.210 Angle : 0.574 11.499 40653 Z= 0.287 Chirality : 0.045 0.405 4748 Planarity : 0.004 0.091 5179 Dihedral : 4.572 32.308 3928 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3615 helix: 1.21 (0.21), residues: 649 sheet: -0.50 (0.17), residues: 928 loop : -1.43 (0.13), residues: 2038 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 12 residues processed: 232 average time/residue: 0.3702 time to fit residues: 147.2712 Evaluate side-chains 211 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 199 time to evaluate : 3.120 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2663 time to fit residues: 10.4076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 6.9990 chunk 315 optimal weight: 0.2980 chunk 69 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 351 optimal weight: 7.9990 chunk 291 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 184 optimal weight: 0.0050 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A1002 GLN B 437 ASN B 448 ASN B1005 GLN C 417 ASN C 493 GLN C 658 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 29852 Z= 0.231 Angle : 0.582 11.162 40653 Z= 0.291 Chirality : 0.045 0.401 4748 Planarity : 0.004 0.126 5179 Dihedral : 4.544 33.753 3928 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3615 helix: 1.29 (0.21), residues: 654 sheet: -0.66 (0.17), residues: 947 loop : -1.39 (0.13), residues: 2014 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 210 time to evaluate : 2.861 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 228 average time/residue: 0.4001 time to fit residues: 154.2949 Evaluate side-chains 205 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 195 time to evaluate : 3.262 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2769 time to fit residues: 9.9304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 338 optimal weight: 0.0030 chunk 39 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 198 optimal weight: 0.3980 chunk 295 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 349 optimal weight: 8.9990 chunk 218 optimal weight: 7.9990 chunk 213 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 804 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN B 448 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN P 35 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 29852 Z= 0.277 Angle : 0.600 11.476 40653 Z= 0.300 Chirality : 0.046 0.400 4748 Planarity : 0.004 0.060 5179 Dihedral : 4.577 32.463 3928 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.08 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.98 (0.14), residues: 3615 helix: 1.35 (0.21), residues: 648 sheet: -0.55 (0.17), residues: 932 loop : -1.40 (0.13), residues: 2035 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 208 time to evaluate : 3.218 Fit side-chains outliers start: 23 outliers final: 9 residues processed: 228 average time/residue: 0.3931 time to fit residues: 151.8104 Evaluate side-chains 201 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 3.250 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2909 time to fit residues: 9.2767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 208 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 222 optimal weight: 0.0170 chunk 238 optimal weight: 7.9990 chunk 172 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 275 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 417 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN P 35 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 29852 Z= 0.159 Angle : 0.564 11.567 40653 Z= 0.281 Chirality : 0.044 0.381 4748 Planarity : 0.004 0.050 5179 Dihedral : 4.405 26.231 3928 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.91 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.88 (0.14), residues: 3615 helix: 1.51 (0.21), residues: 647 sheet: -0.54 (0.17), residues: 934 loop : -1.34 (0.13), residues: 2034 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 209 time to evaluate : 3.113 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 217 average time/residue: 0.3968 time to fit residues: 144.1135 Evaluate side-chains 195 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 3.095 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2653 time to fit residues: 6.8062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 318 optimal weight: 6.9990 chunk 335 optimal weight: 9.9990 chunk 305 optimal weight: 0.5980 chunk 326 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 308 optimal weight: 8.9990 chunk 324 optimal weight: 5.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1135 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 580 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 655 HIS ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1119 ASN U 6 GLN ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN P 35 ASN P 82 GLN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.102 29852 Z= 0.622 Angle : 0.806 15.471 40653 Z= 0.403 Chirality : 0.053 0.435 4748 Planarity : 0.005 0.051 5179 Dihedral : 5.252 31.580 3928 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.69 % Favored : 93.28 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 3615 helix: 0.89 (0.20), residues: 661 sheet: -0.52 (0.17), residues: 894 loop : -1.69 (0.13), residues: 2060 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 216 time to evaluate : 2.874 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 231 average time/residue: 0.4085 time to fit residues: 156.6453 Evaluate side-chains 196 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 3.138 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2712 time to fit residues: 8.1340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 214 optimal weight: 0.8980 chunk 344 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 239 optimal weight: 4.9990 chunk 361 optimal weight: 5.9990 chunk 332 optimal weight: 20.0000 chunk 287 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 222 optimal weight: 0.0040 chunk 176 optimal weight: 0.5980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 448 ASN B 580 GLN B 755 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN U 6 GLN ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN P 35 ASN S 31 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 29852 Z= 0.184 Angle : 0.608 11.353 40653 Z= 0.304 Chirality : 0.046 0.389 4748 Planarity : 0.004 0.068 5179 Dihedral : 4.711 30.629 3928 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.40 % Favored : 95.57 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3615 helix: 1.27 (0.21), residues: 646 sheet: -0.64 (0.17), residues: 925 loop : -1.46 (0.13), residues: 2044 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 204 time to evaluate : 3.165 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 206 average time/residue: 0.3915 time to fit residues: 136.4792 Evaluate side-chains 190 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 3.056 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2693 time to fit residues: 5.8281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 228 optimal weight: 3.9990 chunk 306 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 80 optimal weight: 0.0000 chunk 288 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 296 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 239 GLN B 448 ASN B 755 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1002 GLN ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN P 35 ASN P 82 GLN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.149591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.111024 restraints weight = 53386.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.105562 restraints weight = 86897.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.102239 restraints weight = 84350.347| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 29852 Z= 0.258 Angle : 0.617 11.369 40653 Z= 0.307 Chirality : 0.046 0.381 4748 Planarity : 0.004 0.051 5179 Dihedral : 4.651 29.597 3928 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.12 % Favored : 94.85 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3615 helix: 1.36 (0.21), residues: 647 sheet: -0.65 (0.17), residues: 925 loop : -1.46 (0.13), residues: 2043 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4694.98 seconds wall clock time: 87 minutes 41.32 seconds (5261.32 seconds total)