Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 16 11:53:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czx_30520/07_2023/7czx_30520.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czx_30520/07_2023/7czx_30520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czx_30520/07_2023/7czx_30520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czx_30520/07_2023/7czx_30520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czx_30520/07_2023/7czx_30520.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czx_30520/07_2023/7czx_30520.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 138 5.16 5 C 22132 2.51 5 N 5680 2.21 5 O 6929 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 16": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "K GLU 171": "OE1" <-> "OE2" Residue "K PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 6": "OE1" <-> "OE2" Residue "I GLU 16": "OE1" <-> "OE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "M GLU 171": "OE1" <-> "OE2" Residue "M PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 6": "OE1" <-> "OE2" Residue "J GLU 16": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "N GLU 61": "OE1" <-> "OE2" Residue "N GLU 87": "OE1" <-> "OE2" Residue "N GLU 171": "OE1" <-> "OE2" Residue "N PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 34879 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7866 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "C" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7866 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "H" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1732 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 16, 'TRANS': 213} Chain: "K" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1698 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "I" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1732 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 16, 'TRANS': 213} Chain: "M" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1698 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "J" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1732 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 16, 'TRANS': 213} Chain: "N" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1698 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: 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: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "M" 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: 15.44, per 1000 atoms: 0.44 Number of scatterers: 34879 At special positions: 0 Unit cell: (139.136, 216.313, 241.314, 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 138 16.00 O 6929 8.00 N 5680 7.00 C 22132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.45 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.16 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=1.56 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.33 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS 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=2.29 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.17 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=1.56 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.30 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.51 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.65 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=1.56 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.85 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 94 " distance=1.93 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 200 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.04 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 94 " distance=1.93 Simple disulfide: pdb=" SG CYS M 140 " - pdb=" SG CYS M 200 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.04 Simple disulfide: pdb=" SG CYS J 155 " - pdb=" SG CYS J 211 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 94 " distance=1.93 Simple disulfide: pdb=" SG CYS N 140 " - pdb=" SG CYS N 200 " 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 A1406 " - " NAG A1407 " " NAG B1406 " - " NAG B1407 " " NAG B1411 " - " NAG B1412 " " NAG C1406 " - " NAG M 301 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 343 " " NAG A1409 " - " ASN A 616 " " NAG A1410 " - " ASN A 657 " " NAG A1411 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 343 " " NAG B1408 " - " ASN B 603 " " NAG B1409 " - " ASN B 616 " " NAG B1410 " - " ASN B 657 " " NAG B1411 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 343 " " NAG C1407 " - " ASN C 603 " " NAG C1408 " - " ASN C 616 " " NAG C1409 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 709 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 709 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1074 " " NAG a 1 " - " ASN C1098 " " NAG b 1 " - " ASN C1134 " Time building additional restraints: 12.88 Conformation dependent library (CDL) restraints added in 4.7 seconds 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8160 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 73 sheets defined 17.7% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.075A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.625A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (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: 3.772A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.635A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.648A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.993A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.625A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.633A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.018A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.695A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.546A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.012A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.247A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.075A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.718A 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: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.605A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.589A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (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 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'K' and resid 127 through 134 Processing helix chain 'K' and resid 189 through 193 Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'M' and resid 127 through 134 Processing helix chain 'M' and resid 189 through 193 Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'N' and resid 127 through 134 Processing helix chain 'N' and resid 189 through 193 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.605A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.539A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.791A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.689A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.096A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 327 through 328 removed outlier: 5.480A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.686A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.539A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.250A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 314 removed outlier: 4.197A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 318 through 319 removed outlier: 3.687A pdb=" N PHE C 318 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.133A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.539A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.246A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.581A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN H 5 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER H 79 " --> pdb=" O SER H 70 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.521A pdb=" N ASN H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.521A pdb=" N ASN H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.007A pdb=" N ALA H 152 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 199 " --> pdb=" O ALA H 152 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 154 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 197 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 156 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER H 195 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS H 158 " --> pdb=" O LEU H 193 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 193 " --> pdb=" O LYS H 158 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.007A pdb=" N ALA H 152 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 199 " --> pdb=" O ALA H 152 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 154 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 197 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 156 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER H 195 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS H 158 " --> pdb=" O LEU H 193 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 193 " --> pdb=" O LYS H 158 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 165 through 169 Processing sheet with id=AF5, first strand: chain 'K' and resid 20 through 23 removed outlier: 3.913A pdb=" N ILE K 21 " --> pdb=" O LEU K 79 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU K 79 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE K 77 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR K 78 " --> pdb=" O SER K 71 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 51 through 54 removed outlier: 6.386A pdb=" N TRP K 41 " --> pdb=" O LEU K 53 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 120 through 124 Processing sheet with id=AF8, first strand: chain 'K' and resid 159 through 160 Processing sheet with id=AF9, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.581A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN I 5 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE I 78 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER I 79 " --> pdb=" O SER I 70 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 58 through 59 removed outlier: 3.521A pdb=" N ASN I 58 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 58 through 59 removed outlier: 3.521A pdb=" N ASN I 58 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.007A pdb=" N ALA I 152 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL I 199 " --> pdb=" O ALA I 152 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 154 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL I 197 " --> pdb=" O GLY I 154 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 156 " --> pdb=" O SER I 195 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER I 195 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS I 158 " --> pdb=" O LEU I 193 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 193 " --> pdb=" O LYS I 158 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.007A pdb=" N ALA I 152 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL I 199 " --> pdb=" O ALA I 152 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 154 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL I 197 " --> pdb=" O GLY I 154 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 156 " --> pdb=" O SER I 195 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER I 195 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS I 158 " --> pdb=" O LEU I 193 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 193 " --> pdb=" O LYS I 158 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 165 through 169 Processing sheet with id=AG6, first strand: chain 'M' and resid 20 through 23 removed outlier: 3.914A pdb=" N ILE M 21 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU M 79 " --> pdb=" O ILE M 21 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE M 77 " --> pdb=" O CYS M 23 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR M 78 " --> pdb=" O SER M 71 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 51 through 54 removed outlier: 6.386A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 120 through 124 Processing sheet with id=AG9, first strand: chain 'M' and resid 159 through 160 Processing sheet with id=AH1, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.581A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN J 5 " --> pdb=" O THR J 23 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE J 78 " --> pdb=" O CYS J 22 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER J 79 " --> pdb=" O SER J 70 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 58 through 59 removed outlier: 3.520A pdb=" N ASN J 58 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 58 through 59 removed outlier: 3.520A pdb=" N ASN J 58 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 135 through 139 removed outlier: 5.007A pdb=" N ALA J 152 " --> pdb=" O VAL J 199 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL J 199 " --> pdb=" O ALA J 152 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 154 " --> pdb=" O VAL J 197 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL J 197 " --> pdb=" O GLY J 154 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 156 " --> pdb=" O SER J 195 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER J 195 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS J 158 " --> pdb=" O LEU J 193 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 193 " --> pdb=" O LYS J 158 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 135 through 139 removed outlier: 5.007A pdb=" N ALA J 152 " --> pdb=" O VAL J 199 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL J 199 " --> pdb=" O ALA J 152 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 154 " --> pdb=" O VAL J 197 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL J 197 " --> pdb=" O GLY J 154 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 156 " --> pdb=" O SER J 195 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER J 195 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS J 158 " --> pdb=" O LEU J 193 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 193 " --> pdb=" O LYS J 158 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 165 through 169 Processing sheet with id=AH7, first strand: chain 'N' and resid 20 through 23 removed outlier: 3.914A pdb=" N ILE N 21 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU N 79 " --> pdb=" O ILE N 21 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE N 77 " --> pdb=" O CYS N 23 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR N 78 " --> pdb=" O SER N 71 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'N' and resid 51 through 54 removed outlier: 6.385A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 120 through 124 Processing sheet with id=AI1, first strand: chain 'N' and resid 159 through 160 1234 hydrogen bonds defined for protein. 3255 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: 18.04 Time building geometry restraints manager: 14.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7166 1.32 - 1.46: 10991 1.46 - 1.59: 17337 1.59 - 1.72: 0 1.72 - 1.85: 168 Bond restraints: 35662 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.442 0.080 1.20e-02 6.94e+03 4.45e+01 bond pdb=" CA ILE A 692 " pdb=" C ILE A 692 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.16e-02 7.43e+03 2.91e+01 bond pdb=" CA ILE A 693 " pdb=" CB ILE A 693 " ideal model delta sigma weight residual 1.544 1.472 0.072 1.49e-02 4.50e+03 2.34e+01 bond pdb=" N ILE A 692 " pdb=" CA ILE A 692 " ideal model delta sigma weight residual 1.458 1.403 0.055 1.17e-02 7.31e+03 2.24e+01 bond pdb=" C GLN B 321 " pdb=" N PRO B 322 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.31e-02 5.83e+03 2.05e+01 ... (remaining 35657 not shown) Histogram of bond angle deviations from ideal: 97.58 - 105.74: 782 105.74 - 113.90: 20693 113.90 - 122.06: 20126 122.06 - 130.22: 6783 130.22 - 138.38: 161 Bond angle restraints: 48545 Sorted by residual: angle pdb=" N ILE A 692 " pdb=" CA ILE A 692 " pdb=" C ILE A 692 " ideal model delta sigma weight residual 109.55 100.42 9.13 1.38e+00 5.25e-01 4.37e+01 angle pdb=" N ASP H 111 " pdb=" CA ASP H 111 " pdb=" C ASP H 111 " ideal model delta sigma weight residual 114.64 104.59 10.05 1.52e+00 4.33e-01 4.37e+01 angle pdb=" N ASP I 111 " pdb=" CA ASP I 111 " pdb=" C ASP I 111 " ideal model delta sigma weight residual 114.64 104.60 10.04 1.52e+00 4.33e-01 4.36e+01 angle pdb=" N ASP J 111 " pdb=" CA ASP J 111 " pdb=" C ASP J 111 " ideal model delta sigma weight residual 114.64 104.62 10.02 1.52e+00 4.33e-01 4.34e+01 angle pdb=" CA ILE A 692 " pdb=" C ILE A 692 " pdb=" N ILE A 693 " ideal model delta sigma weight residual 115.82 124.84 -9.02 1.52e+00 4.33e-01 3.52e+01 ... (remaining 48540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17843 17.95 - 35.90: 2052 35.90 - 53.85: 581 53.85 - 71.81: 165 71.81 - 89.76: 65 Dihedral angle restraints: 20706 sinusoidal: 8001 harmonic: 12705 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.03 71.97 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.08 71.92 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.10 71.90 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 20703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5696 0.328 - 0.657: 9 0.657 - 0.985: 9 0.985 - 1.313: 0 1.313 - 1.642: 1 Chirality restraints: 5715 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-02 2.50e+03 1.78e+03 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-02 2.50e+03 1.48e+03 chirality pdb=" C1 NAG B1412 " pdb=" O4 NAG B1411 " pdb=" C2 NAG B1412 " pdb=" O5 NAG B1412 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 ... (remaining 5712 not shown) Planarity restraints: 6202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.131 2.00e-02 2.50e+03 1.94e-01 4.68e+02 pdb=" CG ASN B 331 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.343 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " 0.089 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" CG ASN B 343 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " -0.187 2.00e-02 2.50e+03 pdb=" C1 NAG B1406 " 0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " -0.089 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" CG ASN C 343 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " 0.187 2.00e-02 2.50e+03 pdb=" C1 NAG C1406 " -0.133 2.00e-02 2.50e+03 ... (remaining 6199 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 366 2.51 - 3.11: 25617 3.11 - 3.71: 50080 3.71 - 4.30: 75525 4.30 - 4.90: 125542 Nonbonded interactions: 277130 Sorted by model distance: nonbonded pdb=" O THR B 523 " pdb=" CG1 VAL B 524 " model vdw 1.913 3.460 nonbonded pdb=" NE2 GLN C 675 " pdb=" OG1 THR C 676 " model vdw 2.017 2.520 nonbonded pdb=" O THR A 523 " pdb=" O VAL A 524 " model vdw 2.036 3.040 nonbonded pdb=" O ASN K 143 " pdb=" O ASN K 144 " model vdw 2.038 3.040 nonbonded pdb=" O ASN N 143 " pdb=" O ASN N 144 " model vdw 2.038 3.040 ... (remaining 277125 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 939 or resid 944 through 1146 or resid 1401 thr \ ough 1409)) selection = (chain 'B' and (resid 27 through 826 or resid 855 through 1146 or resid 1401 thr \ ough 1409)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1146 or resid 1401 thr \ ough 1409)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = (chain 'M' and resid 1 through 220) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.630 Check model and map are aligned: 0.560 Set scattering table: 0.320 Process input model: 86.850 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.530 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:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 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 : 0.011 0.116 35662 Z= 0.700 Angle : 1.095 13.379 48545 Z= 0.635 Chirality : 0.073 1.642 5715 Planarity : 0.007 0.082 6155 Dihedral : 17.786 89.757 12393 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 29.18 Ramachandran Plot: Outliers : 3.46 % Allowed : 11.02 % Favored : 85.52 % Rotamer Outliers : 11.08 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.11), residues: 4302 helix: -2.32 (0.16), residues: 701 sheet: -1.81 (0.13), residues: 1320 loop : -3.33 (0.11), residues: 2281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 424 poor density : 444 time to evaluate : 3.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 424 outliers final: 100 residues processed: 817 average time/residue: 1.1377 time to fit residues: 1171.5551 Evaluate side-chains 308 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 208 time to evaluate : 3.596 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 96 residues processed: 4 average time/residue: 0.5347 time to fit residues: 8.1474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 367 optimal weight: 10.0000 chunk 329 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 340 optimal weight: 20.0000 chunk 131 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 253 optimal weight: 0.9990 chunk 395 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 134 GLN A 137 ASN A 188 ASN A 334 ASN A 360 ASN A 388 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 603 ASN A 644 GLN A 658 ASN A 675 GLN A 751 ASN A 762 GLN A 804 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 949 GLN A 954 GLN A 955 ASN A 957 GLN A 969 ASN A 992 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 164 ASN B 188 ASN B 314 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 440 ASN B 450 ASN B 498 GLN B 563 GLN B 644 GLN B 703 ASN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 935 GLN B1002 GLN B1054 GLN C 52 GLN C 125 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 188 ASN C 239 GLN C 360 ASN C 394 ASN C 422 ASN C 440 ASN C 450 ASN C 532 ASN C 540 ASN C 644 GLN C 690 GLN C 703 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C1010 GLN C1071 GLN C1101 HIS H 108 GLN H 179 HIS K 22 ASN K 44 GLN I 212 ASN M 22 ASN M 44 GLN J 212 ASN N 22 ASN N 44 GLN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.097 35662 Z= 0.275 Angle : 0.823 13.838 48545 Z= 0.411 Chirality : 0.051 0.416 5715 Planarity : 0.006 0.075 6155 Dihedral : 5.657 29.456 4674 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.76 % Favored : 90.79 % Rotamer Outliers : 7.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.12), residues: 4302 helix: -0.32 (0.19), residues: 701 sheet: -1.12 (0.14), residues: 1277 loop : -2.75 (0.11), residues: 2324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 247 time to evaluate : 4.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 283 outliers final: 115 residues processed: 492 average time/residue: 1.0487 time to fit residues: 664.7721 Evaluate side-chains 307 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 192 time to evaluate : 3.753 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 104 residues processed: 13 average time/residue: 0.5899 time to fit residues: 16.6643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 219 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 328 optimal weight: 8.9990 chunk 268 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 395 optimal weight: 5.9990 chunk 427 optimal weight: 20.0000 chunk 352 optimal weight: 30.0000 chunk 392 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 317 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 703 ASN A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 314 GLN B 394 ASN B 501 ASN B 703 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 49 HIS C 125 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 498 GLN C 613 GLN C 658 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 ASN M 27 GLN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.105 35662 Z= 0.379 Angle : 0.805 11.740 48545 Z= 0.398 Chirality : 0.052 0.417 5715 Planarity : 0.005 0.069 6155 Dihedral : 5.491 31.438 4674 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.32 % Favored : 90.28 % Rotamer Outliers : 6.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.24 (0.12), residues: 4302 helix: 0.15 (0.19), residues: 702 sheet: -0.84 (0.14), residues: 1318 loop : -2.51 (0.11), residues: 2282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 224 time to evaluate : 3.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 264 outliers final: 141 residues processed: 452 average time/residue: 1.0335 time to fit residues: 605.0352 Evaluate side-chains 321 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 180 time to evaluate : 3.870 Switching outliers to nearest non-outliers outliers start: 141 outliers final: 128 residues processed: 13 average time/residue: 0.6714 time to fit residues: 17.7712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 390 optimal weight: 0.2980 chunk 297 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 188 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 397 optimal weight: 1.9990 chunk 420 optimal weight: 40.0000 chunk 207 optimal weight: 10.0000 chunk 376 optimal weight: 30.0000 chunk 113 optimal weight: 8.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A1005 GLN B 49 HIS B 134 GLN B 314 GLN B 703 ASN B 787 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 ASN M 48 GLN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 166 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 35662 Z= 0.208 Angle : 0.710 15.927 48545 Z= 0.345 Chirality : 0.047 0.349 5715 Planarity : 0.005 0.059 6155 Dihedral : 5.100 30.870 4674 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.67 % Favored : 91.98 % Rotamer Outliers : 6.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.12), residues: 4302 helix: 0.74 (0.20), residues: 700 sheet: -0.50 (0.14), residues: 1307 loop : -2.29 (0.11), residues: 2295 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 210 time to evaluate : 3.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 239 outliers final: 131 residues processed: 421 average time/residue: 1.0358 time to fit residues: 565.9360 Evaluate side-chains 305 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 174 time to evaluate : 3.731 Switching outliers to nearest non-outliers outliers start: 131 outliers final: 125 residues processed: 6 average time/residue: 0.9255 time to fit residues: 12.4144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 350 optimal weight: 30.0000 chunk 238 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 313 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 358 optimal weight: 8.9990 chunk 290 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 chunk 377 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1005 GLN B 115 GLN B 314 GLN B 690 GLN B 935 GLN B 992 GLN B1002 GLN B1010 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 804 GLN C 992 GLN C1005 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 ASN K 164 ASN K 166 GLN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 143 ASN J 60 ASN N 166 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.118 35662 Z= 0.412 Angle : 0.792 17.234 48545 Z= 0.387 Chirality : 0.052 0.406 5715 Planarity : 0.005 0.059 6155 Dihedral : 5.373 28.859 4674 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.14 % Favored : 90.52 % Rotamer Outliers : 6.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.12), residues: 4302 helix: 0.55 (0.20), residues: 709 sheet: -0.50 (0.14), residues: 1307 loop : -2.27 (0.12), residues: 2286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 190 time to evaluate : 3.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 257 outliers final: 155 residues processed: 415 average time/residue: 1.0134 time to fit residues: 550.4484 Evaluate side-chains 314 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 159 time to evaluate : 3.649 Switching outliers to nearest non-outliers outliers start: 155 outliers final: 139 residues processed: 16 average time/residue: 0.7775 time to fit residues: 22.0469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 141 optimal weight: 7.9990 chunk 378 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 246 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 420 optimal weight: 0.6980 chunk 349 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 139 optimal weight: 20.0000 chunk 220 optimal weight: 8.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A 957 GLN B 207 HIS B 498 GLN B 613 GLN B 935 GLN B1002 GLN B1010 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C1005 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 ASN K 164 ASN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 35662 Z= 0.363 Angle : 0.766 18.912 48545 Z= 0.375 Chirality : 0.051 0.395 5715 Planarity : 0.005 0.074 6155 Dihedral : 5.309 29.742 4674 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.41 % Favored : 91.33 % Rotamer Outliers : 6.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.12), residues: 4302 helix: 0.57 (0.20), residues: 707 sheet: -0.46 (0.14), residues: 1314 loop : -2.25 (0.12), residues: 2281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 188 time to evaluate : 3.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 231 outliers final: 157 residues processed: 392 average time/residue: 1.0064 time to fit residues: 521.7574 Evaluate side-chains 319 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 162 time to evaluate : 3.882 Switching outliers to nearest non-outliers outliers start: 157 outliers final: 142 residues processed: 15 average time/residue: 0.6185 time to fit residues: 19.0935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 405 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 239 optimal weight: 10.0000 chunk 307 optimal weight: 20.0000 chunk 238 optimal weight: 9.9990 chunk 354 optimal weight: 30.0000 chunk 235 optimal weight: 30.0000 chunk 419 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 chunk 193 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 954 GLN A 957 GLN A1113 GLN B 207 HIS B 498 GLN B 703 ASN B 935 GLN B 957 GLN B1002 GLN B1010 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 ASN K 164 ASN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 161 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 35662 Z= 0.242 Angle : 0.705 16.954 48545 Z= 0.344 Chirality : 0.048 0.358 5715 Planarity : 0.005 0.058 6155 Dihedral : 5.028 29.708 4674 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.90 % Favored : 91.84 % Rotamer Outliers : 5.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.12), residues: 4302 helix: 0.98 (0.20), residues: 694 sheet: -0.27 (0.14), residues: 1254 loop : -2.12 (0.12), residues: 2354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 179 time to evaluate : 3.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 194 outliers final: 145 residues processed: 354 average time/residue: 1.0137 time to fit residues: 471.9929 Evaluate side-chains 301 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 156 time to evaluate : 3.880 Switching outliers to nearest non-outliers outliers start: 145 outliers final: 139 residues processed: 6 average time/residue: 0.9967 time to fit residues: 12.8686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 259 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 250 optimal weight: 0.7980 chunk 126 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 266 optimal weight: 0.9980 chunk 285 optimal weight: 0.7980 chunk 207 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 329 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 954 GLN A 957 GLN B 422 ASN B 498 GLN B 935 GLN B1002 GLN B1010 GLN C 121 ASN C 134 GLN C1005 GLN K 6 GLN ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 ASN K 164 ASN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 35662 Z= 0.179 Angle : 0.670 16.047 48545 Z= 0.326 Chirality : 0.047 0.322 5715 Planarity : 0.005 0.061 6155 Dihedral : 4.776 29.139 4674 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.35 % Favored : 92.40 % Rotamer Outliers : 4.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.12), residues: 4302 helix: 1.28 (0.20), residues: 696 sheet: -0.17 (0.14), residues: 1317 loop : -2.04 (0.12), residues: 2289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 177 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 187 outliers final: 134 residues processed: 348 average time/residue: 1.0295 time to fit residues: 470.9278 Evaluate side-chains 297 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 163 time to evaluate : 4.147 Switching outliers to nearest non-outliers outliers start: 134 outliers final: 128 residues processed: 6 average time/residue: 0.8269 time to fit residues: 12.2549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 381 optimal weight: 20.0000 chunk 401 optimal weight: 9.9990 chunk 366 optimal weight: 8.9990 chunk 390 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 306 optimal weight: 20.0000 chunk 119 optimal weight: 0.9990 chunk 353 optimal weight: 30.0000 chunk 369 optimal weight: 9.9990 chunk 389 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 188 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 498 GLN B 935 GLN B 957 GLN B1002 GLN B1010 GLN C1005 GLN C1010 GLN K 143 ASN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 35662 Z= 0.222 Angle : 0.690 16.041 48545 Z= 0.337 Chirality : 0.047 0.334 5715 Planarity : 0.005 0.061 6155 Dihedral : 4.773 28.486 4674 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.62 % Favored : 92.14 % Rotamer Outliers : 4.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.12), residues: 4302 helix: 1.21 (0.20), residues: 696 sheet: -0.16 (0.14), residues: 1312 loop : -1.98 (0.12), residues: 2294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 168 time to evaluate : 4.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 167 outliers final: 132 residues processed: 324 average time/residue: 1.0308 time to fit residues: 444.2647 Evaluate side-chains 287 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 155 time to evaluate : 3.880 Switching outliers to nearest non-outliers outliers start: 132 outliers final: 128 residues processed: 4 average time/residue: 1.1084 time to fit residues: 11.0909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 256 optimal weight: 0.0010 chunk 413 optimal weight: 6.9990 chunk 252 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 chunk 287 optimal weight: 4.9990 chunk 433 optimal weight: 40.0000 chunk 398 optimal weight: 20.0000 chunk 345 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 266 optimal weight: 0.8980 chunk 211 optimal weight: 0.8980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 935 GLN B1002 GLN B1010 GLN K 143 ASN K 164 ASN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 143 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 35662 Z= 0.202 Angle : 0.675 15.895 48545 Z= 0.328 Chirality : 0.047 0.323 5715 Planarity : 0.005 0.061 6155 Dihedral : 4.680 27.735 4674 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.35 % Favored : 92.45 % Rotamer Outliers : 3.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 4302 helix: 1.29 (0.20), residues: 694 sheet: -0.11 (0.14), residues: 1312 loop : -1.91 (0.12), residues: 2296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 163 time to evaluate : 4.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 131 residues processed: 306 average time/residue: 0.9703 time to fit residues: 393.4777 Evaluate side-chains 300 residues out of total 3825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 169 time to evaluate : 3.831 Switching outliers to nearest non-outliers outliers start: 131 outliers final: 127 residues processed: 5 average time/residue: 0.6536 time to fit residues: 10.0224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 274 optimal weight: 0.9980 chunk 367 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 318 optimal weight: 9.9990 chunk 50 optimal weight: 0.3980 chunk 95 optimal weight: 0.7980 chunk 345 optimal weight: 3.9990 chunk 144 optimal weight: 0.2980 chunk 354 optimal weight: 50.0000 chunk 43 optimal weight: 30.0000 chunk 63 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 856 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 935 GLN B 957 GLN B1002 GLN B1010 GLN C 125 ASN ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN K 143 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.223991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.178352 restraints weight = 50179.714| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.93 r_work: 0.3321 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 35662 Z= 0.187 Angle : 0.664 15.045 48545 Z= 0.322 Chirality : 0.046 0.317 5715 Planarity : 0.004 0.059 6155 Dihedral : 4.626 30.264 4674 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.51 % Favored : 92.28 % Rotamer Outliers : 3.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: -1.09 (0.13), residues: 4302 helix: 1.38 (0.20), residues: 693 sheet: -0.09 (0.14), residues: 1321 loop : -1.86 (0.12), residues: 2288 =============================================================================== Job complete usr+sys time: 10352.06 seconds wall clock time: 186 minutes 44.68 seconds (11204.68 seconds total)