Starting phenix.real_space_refine on Thu Mar 21 19:34:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czw_30519/03_2024/7czw_30519.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czw_30519/03_2024/7czw_30519.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/7czw_30519/03_2024/7czw_30519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czw_30519/03_2024/7czw_30519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czw_30519/03_2024/7czw_30519.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czw_30519/03_2024/7czw_30519.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 19667 2.51 5 N 5060 2.21 5 O 6148 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 ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" 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 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "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 GLU 96": "OE1" <-> "OE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C GLU 154": "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 GLU 224": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" 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 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 "L GLU 165": "OE1" <-> "OE2" Residue "L GLU 188": "OE1" <-> "OE2" Residue "L GLU 208": "OE1" <-> "OE2" Residue "J GLU 6": "OE1" <-> "OE2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "N GLU 188": "OE1" <-> "OE2" Residue "N GLU 208": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31004 Number of models: 1 Model: "" Number of chains: 31 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: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7696 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 47, 'TRANS': 934} Chain breaks: 11 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1727 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 16, 'TRANS': 213} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1579 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 14, 'TRANS': 199} Chain: "J" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1727 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 16, 'TRANS': 213} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1579 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 14, 'TRANS': 199} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 16.41, per 1000 atoms: 0.53 Number of scatterers: 31004 At special positions: 0 Unit cell: (134.788, 169.572, 250.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 6148 8.00 N 5060 7.00 C 19667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.33 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.36 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.17 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 112 " distance=2.19 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 97 " distance=2.04 Simple disulfide: pdb=" SG CYS J 102 " - pdb=" SG CYS J 112 " distance=2.19 Simple disulfide: pdb=" SG CYS J 155 " - pdb=" SG CYS J 211 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 139 " - pdb=" SG CYS N 198 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B1410 " - " NAG B1411 " " 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 I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 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 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " 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 B1407 " - " ASN B 603 " " NAG B1408 " - " ASN B 616 " " NAG B1409 " - " ASN B 657 " " NAG B1410 " - " 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 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 709 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 331 " " NAG V 1 " - " ASN C 343 " " 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: 11.46 Conformation dependent library (CDL) restraints added in 5.2 seconds 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7244 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 64 sheets defined 19.5% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A 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: 3.860A 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: 3.631A 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: 3.771A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.641A 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: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.633A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.538A 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: 3.647A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.575A 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: 3.693A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.647A 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: 4.632A 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: 3.647A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.646A 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 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.640A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 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: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A 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: 3.543A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.602A 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: 3.846A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A 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: 3.704A 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: 4.372A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.120A 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: 3.582A 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: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.625A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.861A 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 616 through 620 removed outlier: 3.582A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A 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: 3.721A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.604A 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: 3.590A 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: 3.712A 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: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.554A 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: 3.755A 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: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.634A 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 88 through 92 removed outlier: 3.947A pdb=" N ASP H 91 " --> pdb=" O THR H 88 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 88 through 92' Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 186 through 193 Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.947A pdb=" N ASP J 91 " --> pdb=" O THR J 88 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR J 92 " --> pdb=" O ALA J 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 88 through 92' 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 126 through 132 Processing helix chain 'N' and resid 186 through 193 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A 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: 4.437A 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 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.570A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A 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: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A 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: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.679A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) 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 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.338A 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) removed outlier: 6.949A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.256A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.624A 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=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, 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: 6.830A 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: 3.529A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.969A 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=AB5, 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: 6.830A 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: 3.978A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.728A 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: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, 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=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, 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=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.538A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.074A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.649A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.779A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.572A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.421A 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: 6.769A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.168A 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=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A 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: 3.799A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, 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=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.151A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.756A pdb=" N THR C 274 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS C 291 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.248A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.666A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, 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=AE1, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.865A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 543 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.231A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (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: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A 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=AE6, 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: 3.880A 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=AE7, 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=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.444A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 98 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR H 95 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR H 122 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.008A pdb=" N ALA H 152 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 6.765A 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: 7.048A pdb=" N VAL H 197 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU H 156 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 7.180A 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: 6.573A 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: 5.008A pdb=" N ALA H 152 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 6.765A 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: 7.048A pdb=" N VAL H 197 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU H 156 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 7.180A 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: 6.573A 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 'L' and resid 9 through 12 removed outlier: 6.973A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET L 49 " --> pdb=" O TRP L 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF7, first strand: chain 'L' and resid 119 through 123 Processing sheet with id=AF8, first strand: chain 'L' and resid 119 through 123 Processing sheet with id=AF9, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.441A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'J' and resid 59 through 61 removed outlier: 5.445A pdb=" N TRP J 49 " --> pdb=" O ARG J 40 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG J 40 " --> pdb=" O TRP J 49 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY J 51 " --> pdb=" O TRP J 38 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA J 98 " --> pdb=" O SER J 37 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR J 95 " --> pdb=" O THR J 122 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR J 122 " --> pdb=" O TYR J 95 " (cutoff:3.500A) Processing sheet with id=AG3, 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: 6.764A pdb=" N VAL J 199 " --> pdb=" O ALA J 152 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 154 " --> pdb=" O VAL J 197 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL J 197 " --> pdb=" O GLY J 154 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU J 156 " --> pdb=" O SER J 195 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 195 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 158 " --> pdb=" O LEU J 193 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU J 193 " --> pdb=" O LYS J 158 " (cutoff:3.500A) Processing sheet with id=AG4, 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: 6.764A pdb=" N VAL J 199 " --> pdb=" O ALA J 152 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 154 " --> pdb=" O VAL J 197 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL J 197 " --> pdb=" O GLY J 154 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU J 156 " --> pdb=" O SER J 195 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 195 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 158 " --> pdb=" O LEU J 193 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU J 193 " --> pdb=" O LYS J 158 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 165 through 169 Processing sheet with id=AG6, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.972A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET N 49 " --> pdb=" O TRP N 37 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AG8, first strand: chain 'N' and resid 119 through 123 Processing sheet with id=AG9, first strand: chain 'N' and resid 119 through 123 Processing sheet with id=AH1, first strand: chain 'N' and resid 159 through 160 removed outlier: 4.442A pdb=" N TRP N 153 " --> pdb=" O VAL N 160 " (cutoff:3.500A) 1191 hydrogen bonds defined for protein. 3207 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: 14.57 Time building geometry restraints manager: 12.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9615 1.34 - 1.46: 8183 1.46 - 1.59: 13735 1.59 - 1.72: 0 1.72 - 1.84: 158 Bond restraints: 31691 Sorted by residual: bond pdb=" C THR C 588 " pdb=" N PRO C 589 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.34e-02 5.57e+03 1.82e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.067 1.59e-02 3.96e+03 1.77e+01 bond pdb=" N PRO C 589 " pdb=" CD PRO C 589 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.65e+01 bond pdb=" N PRO L 7 " pdb=" CD PRO L 7 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.57e+01 bond pdb=" N PRO N 7 " pdb=" CD PRO N 7 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.53e+01 ... (remaining 31686 not shown) Histogram of bond angle deviations from ideal: 97.55 - 105.73: 673 105.73 - 113.91: 18493 113.91 - 122.09: 17853 122.09 - 130.27: 6011 130.27 - 138.45: 106 Bond angle restraints: 43136 Sorted by residual: angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.80 -11.26 1.91e+00 2.74e-01 3.48e+01 angle pdb=" N GLU C 156 " pdb=" CA GLU C 156 " pdb=" C GLU C 156 " ideal model delta sigma weight residual 108.45 115.85 -7.40 1.26e+00 6.30e-01 3.45e+01 angle pdb=" C THR C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta sigma weight residual 119.78 114.11 5.67 1.03e+00 9.43e-01 3.03e+01 angle pdb=" C LEU B 212 " pdb=" N VAL B 213 " pdb=" CA VAL B 213 " ideal model delta sigma weight residual 123.08 117.63 5.45 1.01e+00 9.80e-01 2.91e+01 angle pdb=" C SER A 31 " pdb=" N PHE A 32 " pdb=" CA PHE A 32 " ideal model delta sigma weight residual 122.56 115.27 7.29 1.50e+00 4.44e-01 2.36e+01 ... (remaining 43131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17052 17.92 - 35.85: 1940 35.85 - 53.77: 573 53.77 - 71.69: 186 71.69 - 89.61: 59 Dihedral angle restraints: 19810 sinusoidal: 8541 harmonic: 11269 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 12.11 80.89 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 19.63 73.37 1 1.00e+01 1.00e-02 6.85e+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 21.10 71.90 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 19807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 5110 0.329 - 0.658: 3 0.658 - 0.986: 3 0.986 - 1.315: 0 1.315 - 1.644: 1 Chirality restraints: 5117 Sorted by residual: chirality pdb=" C1 NAG B1411 " pdb=" O4 NAG B1410 " pdb=" C2 NAG B1411 " pdb=" O5 NAG B1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.76e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.44 -0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 5114 not shown) Planarity restraints: 5508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA J 109 " 0.062 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO J 110 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO J 110 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO J 110 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 109 " -0.062 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO H 110 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO H 110 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO H 110 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1134 " -0.022 2.00e-02 2.50e+03 3.13e-02 1.22e+01 pdb=" CG ASN C1134 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN C1134 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C1134 " 0.055 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " -0.034 2.00e-02 2.50e+03 ... (remaining 5505 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 360 2.56 - 3.15: 24446 3.15 - 3.73: 45311 3.73 - 4.32: 65650 4.32 - 4.90: 109618 Nonbonded interactions: 245385 Sorted by model distance: nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.981 2.520 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.981 2.520 nonbonded pdb=" O ALA C 522 " pdb=" OG1 THR C 523 " model vdw 2.137 2.440 nonbonded pdb=" O ALA A 522 " pdb=" OG1 THR A 523 " model vdw 2.137 2.440 nonbonded pdb=" O SER A 813 " pdb=" OG SER A 813 " model vdw 2.183 2.440 ... (remaining 245380 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 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 620 or resid 641 through 939 or resid 944 through 11 \ 46 or resid 1401 through 1408)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1408)) selection = (chain 'C' and (resid 27 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 826 or resid 855 through 1146 or resid 1401 through \ 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' 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 'J' } ncs_group { reference = chain 'L' 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.210 Check model and map are aligned: 0.490 Set scattering table: 0.310 Process input model: 83.480 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.430 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:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 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 0.118 31691 Z= 0.694 Angle : 0.996 13.445 43136 Z= 0.567 Chirality : 0.068 1.644 5117 Planarity : 0.007 0.096 5460 Dihedral : 17.561 89.613 12422 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 1.23 % Allowed : 9.99 % Favored : 88.77 % Rotamer: Outliers : 11.42 % Allowed : 19.20 % Favored : 69.38 % 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: -3.75 (0.11), residues: 3812 helix: -2.14 (0.16), residues: 679 sheet: -1.69 (0.14), residues: 1131 loop : -3.17 (0.11), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 104 HIS 0.009 0.002 HIS A1048 PHE 0.025 0.003 PHE A 898 TYR 0.026 0.003 TYR B 265 ARG 0.008 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 3380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 386 poor density : 409 time to evaluate : 3.291 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 TARDY: cannot create tardy model for: "SER H 128 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER J 128 " (corrupted residue). Skipping it. REVERT: A 51 THR cc_start: 0.7986 (p) cc_final: 0.7655 (m) REVERT: A 153 MET cc_start: -0.0525 (mpp) cc_final: -0.2255 (ptp) REVERT: A 785 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8147 (m) REVERT: A 973 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7511 (pp) REVERT: A 1039 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7361 (mtp180) REVERT: B 50 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.7857 (t) REVERT: B 95 THR cc_start: 0.4761 (OUTLIER) cc_final: 0.4494 (p) REVERT: B 153 MET cc_start: 0.0535 (ttp) cc_final: 0.0289 (ttp) REVERT: B 278 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8560 (ttmt) REVERT: B 371 SER cc_start: 0.4996 (OUTLIER) cc_final: 0.4706 (p) REVERT: B 430 THR cc_start: 0.7093 (OUTLIER) cc_final: 0.6711 (m) REVERT: B 514 SER cc_start: 0.5993 (OUTLIER) cc_final: 0.5506 (m) REVERT: B 581 THR cc_start: 0.7561 (p) cc_final: 0.7330 (t) REVERT: B 878 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8831 (tp) REVERT: B 1029 MET cc_start: 0.9146 (tpp) cc_final: 0.8819 (tpp) REVERT: C 117 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6704 (pt) REVERT: C 306 PHE cc_start: 0.7819 (m-80) cc_final: 0.7486 (m-80) REVERT: C 382 VAL cc_start: 0.1613 (OUTLIER) cc_final: 0.1380 (t) REVERT: C 486 PHE cc_start: -0.0015 (OUTLIER) cc_final: -0.0263 (t80) REVERT: C 1027 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8513 (m) REVERT: H 34 TYR cc_start: 0.1876 (m-80) cc_final: 0.1042 (m-80) REVERT: H 120 GLN cc_start: 0.2929 (OUTLIER) cc_final: 0.2353 (pt0) REVERT: L 49 MET cc_start: 0.1579 (pmm) cc_final: -0.1090 (mtt) REVERT: L 75 LEU cc_start: -0.0051 (tp) cc_final: -0.0275 (tt) REVERT: L 97 SER cc_start: 0.1828 (OUTLIER) cc_final: 0.1523 (m) REVERT: L 108 LEU cc_start: -0.0723 (tp) cc_final: -0.0999 (pp) REVERT: L 140 LEU cc_start: 0.0911 (mp) cc_final: 0.0458 (tp) REVERT: L 185 LEU cc_start: 0.0079 (OUTLIER) cc_final: -0.0145 (mm) REVERT: J 120 GLN cc_start: 0.2738 (OUTLIER) cc_final: 0.1610 (pt0) REVERT: N 119 SER cc_start: 0.1390 (OUTLIER) cc_final: 0.1129 (p) REVERT: N 185 LEU cc_start: 0.1878 (OUTLIER) cc_final: 0.1254 (mp) outliers start: 386 outliers final: 85 residues processed: 741 average time/residue: 0.9488 time to fit residues: 885.4593 Evaluate side-chains 313 residues out of total 3380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 208 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain J residue 112 CYS Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 158 SER Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain N residue 192 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 325 optimal weight: 3.9990 chunk 292 optimal weight: 0.9980 chunk 162 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 302 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 225 optimal weight: 8.9990 chunk 350 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 188 ASN A 239 GLN A 422 ASN A 440 ASN A 498 GLN A 542 ASN A 607 GLN A 644 GLN A 690 GLN A 703 ASN A 755 GLN A 762 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 969 ASN A 992 GLN A1005 GLN A1101 HIS A1125 ASN B 115 GLN B 134 GLN B 314 GLN B 409 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 542 ASN B 563 GLN B 690 GLN B 804 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1010 GLN B1054 GLN B1142 GLN C 30 ASN C 66 HIS C 188 ASN C 207 HIS C 321 GLN C 422 ASN C 440 ASN C 498 GLN C 690 GLN C 703 ASN C 751 ASN C 784 GLN C 804 GLN C 901 GLN C 926 GLN C 935 GLN C 957 GLN C 969 ASN C 992 GLN C1005 GLN C1010 GLN C1071 GLN C1101 HIS H 60 ASN H 62 ASN L 39 GLN L 40 GLN L 133 ASN L 193 HIS L 199 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN ** J 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 40 GLN N 193 HIS N 199 GLN ** N 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 31691 Z= 0.233 Angle : 0.761 13.899 43136 Z= 0.379 Chirality : 0.050 0.620 5117 Planarity : 0.005 0.067 5460 Dihedral : 9.650 73.032 5760 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.08 % Favored : 92.68 % Rotamer: Outliers : 6.51 % Allowed : 23.05 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.12), residues: 3812 helix: -0.15 (0.19), residues: 685 sheet: -0.86 (0.15), residues: 1075 loop : -2.58 (0.12), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 38 HIS 0.007 0.001 HIS A 519 PHE 0.026 0.002 PHE B 168 TYR 0.028 0.002 TYR B 453 ARG 0.011 0.001 ARG H 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 229 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER H 128 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER J 128 " (corrupted residue). Skipping it. REVERT: A 51 THR cc_start: 0.7915 (OUTLIER) cc_final: 0.7711 (m) REVERT: A 153 MET cc_start: -0.0736 (mpp) cc_final: -0.2428 (ptp) REVERT: A 304 LYS cc_start: 0.8077 (mttm) cc_final: 0.7791 (mtpt) REVERT: A 389 ASP cc_start: 0.6658 (OUTLIER) cc_final: 0.5087 (t70) REVERT: A 692 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7837 (mm) REVERT: A 1074 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8453 (p0) REVERT: B 164 ASN cc_start: 0.4770 (OUTLIER) cc_final: 0.4188 (t0) REVERT: B 360 ASN cc_start: 0.7625 (m-40) cc_final: 0.7388 (m-40) REVERT: B 389 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6542 (m-30) REVERT: B 430 THR cc_start: 0.7128 (OUTLIER) cc_final: 0.6854 (m) REVERT: B 731 MET cc_start: 0.8340 (mtm) cc_final: 0.8049 (mtm) REVERT: B 752 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8701 (mt) REVERT: B 787 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: B 1029 MET cc_start: 0.9180 (tpp) cc_final: 0.8831 (tpp) REVERT: C 32 PHE cc_start: 0.6694 (m-80) cc_final: 0.6494 (m-10) REVERT: C 86 PHE cc_start: 0.5971 (OUTLIER) cc_final: 0.5595 (t80) REVERT: C 205 SER cc_start: 0.8137 (OUTLIER) cc_final: 0.7891 (t) REVERT: C 306 PHE cc_start: 0.8026 (m-80) cc_final: 0.7685 (m-80) REVERT: C 525 CYS cc_start: 0.2538 (OUTLIER) cc_final: 0.2308 (m) REVERT: H 82 LEU cc_start: 0.0802 (OUTLIER) cc_final: -0.0187 (mp) REVERT: H 193 LEU cc_start: -0.1485 (OUTLIER) cc_final: -0.1759 (mp) REVERT: H 204 LEU cc_start: 0.1340 (mt) cc_final: 0.0891 (pt) REVERT: L 49 MET cc_start: 0.1709 (pmm) cc_final: -0.0670 (mtt) REVERT: L 97 SER cc_start: 0.1707 (OUTLIER) cc_final: 0.1468 (m) REVERT: N 49 MET cc_start: 0.1205 (OUTLIER) cc_final: -0.0964 (ttm) outliers start: 220 outliers final: 80 residues processed: 423 average time/residue: 0.9170 time to fit residues: 493.1942 Evaluate side-chains 290 residues out of total 3380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 194 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain N residue 199 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 194 optimal weight: 0.0010 chunk 108 optimal weight: 0.0270 chunk 291 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 351 optimal weight: 6.9990 chunk 379 optimal weight: 9.9990 chunk 312 optimal weight: 50.0000 chunk 348 optimal weight: 0.3980 chunk 119 optimal weight: 6.9990 chunk 281 optimal weight: 0.0980 overall best weight: 1.3046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 542 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A1005 GLN B 121 ASN B 188 ASN B 422 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN C 134 GLN C 207 HIS C 542 ASN C 580 GLN C 755 GLN C 957 GLN C1005 GLN L 199 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN N 199 GLN ** N 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31691 Z= 0.211 Angle : 0.699 11.815 43136 Z= 0.347 Chirality : 0.049 0.649 5117 Planarity : 0.005 0.055 5460 Dihedral : 8.018 59.916 5659 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.08 % Favored : 92.68 % Rotamer: Outliers : 5.18 % Allowed : 24.47 % Favored : 70.36 % 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: -1.71 (0.13), residues: 3812 helix: 0.73 (0.20), residues: 691 sheet: -0.49 (0.15), residues: 1078 loop : -2.26 (0.12), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 49 HIS 0.003 0.001 HIS A1048 PHE 0.021 0.001 PHE B 168 TYR 0.023 0.001 TYR N 34 ARG 0.009 0.001 ARG J 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 209 time to evaluate : 3.400 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: A 51 THR cc_start: 0.7918 (p) cc_final: 0.7594 (m) REVERT: A 153 MET cc_start: -0.0302 (mpp) cc_final: -0.2296 (ptp) REVERT: A 389 ASP cc_start: 0.6589 (OUTLIER) cc_final: 0.5086 (t70) REVERT: B 164 ASN cc_start: 0.4691 (OUTLIER) cc_final: 0.4253 (t0) REVERT: B 360 ASN cc_start: 0.7982 (m-40) cc_final: 0.7715 (m-40) REVERT: B 389 ASP cc_start: 0.6654 (OUTLIER) cc_final: 0.6288 (m-30) REVERT: B 430 THR cc_start: 0.7284 (OUTLIER) cc_final: 0.7039 (m) REVERT: B 900 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8265 (mtm) REVERT: B 1029 MET cc_start: 0.9233 (tpp) cc_final: 0.8893 (tpp) REVERT: C 32 PHE cc_start: 0.6620 (m-80) cc_final: 0.6399 (m-10) REVERT: C 86 PHE cc_start: 0.5865 (OUTLIER) cc_final: 0.5358 (t80) REVERT: C 306 PHE cc_start: 0.7939 (m-80) cc_final: 0.7646 (m-80) REVERT: C 382 VAL cc_start: 0.1651 (OUTLIER) cc_final: 0.1245 (t) REVERT: C 525 CYS cc_start: 0.3340 (OUTLIER) cc_final: 0.3137 (m) REVERT: C 1129 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8667 (t) REVERT: H 11 LEU cc_start: 0.3008 (OUTLIER) cc_final: 0.2503 (mp) REVERT: H 82 LEU cc_start: 0.1255 (OUTLIER) cc_final: 0.0122 (mp) REVERT: H 204 LEU cc_start: 0.1562 (mt) cc_final: 0.0870 (pt) REVERT: L 49 MET cc_start: 0.1884 (pmm) cc_final: -0.0617 (mtt) REVERT: L 125 PRO cc_start: 0.1893 (Cg_exo) cc_final: 0.1637 (Cg_endo) REVERT: J 198 THR cc_start: 0.1326 (p) cc_final: 0.0991 (t) REVERT: N 49 MET cc_start: 0.1209 (OUTLIER) cc_final: -0.0816 (ttm) outliers start: 175 outliers final: 75 residues processed: 363 average time/residue: 0.9205 time to fit residues: 428.3802 Evaluate side-chains 261 residues out of total 3380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 174 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain N residue 199 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 346 optimal weight: 0.5980 chunk 264 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 235 optimal weight: 30.0000 chunk 352 optimal weight: 6.9990 chunk 373 optimal weight: 20.0000 chunk 184 optimal weight: 0.9990 chunk 334 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 606 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 955 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B1142 GLN C 957 GLN C1005 GLN C1106 GLN L 199 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 GLN ** N 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 31691 Z= 0.264 Angle : 0.718 12.406 43136 Z= 0.354 Chirality : 0.050 0.591 5117 Planarity : 0.005 0.054 5460 Dihedral : 7.646 59.638 5649 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.11 % Favored : 92.63 % Rotamer: Outliers : 5.30 % Allowed : 24.23 % Favored : 70.47 % 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: -1.45 (0.13), residues: 3812 helix: 0.97 (0.21), residues: 690 sheet: -0.31 (0.15), residues: 1090 loop : -2.11 (0.12), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 190 HIS 0.004 0.001 HIS A1048 PHE 0.023 0.002 PHE B 168 TYR 0.023 0.002 TYR H 35 ARG 0.005 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 201 time to evaluate : 3.404 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: A 51 THR cc_start: 0.8014 (p) cc_final: 0.7600 (m) REVERT: A 153 MET cc_start: 0.0032 (mpp) cc_final: -0.2080 (ptp) REVERT: A 692 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8335 (mm) REVERT: A 964 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7807 (mppt) REVERT: A 1010 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7775 (mp10) REVERT: B 127 VAL cc_start: 0.7498 (m) cc_final: 0.7298 (t) REVERT: B 164 ASN cc_start: 0.4911 (OUTLIER) cc_final: 0.4531 (t0) REVERT: B 389 ASP cc_start: 0.6680 (OUTLIER) cc_final: 0.6290 (m-30) REVERT: B 455 LEU cc_start: 0.3203 (OUTLIER) cc_final: 0.2448 (tp) REVERT: B 528 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6884 (tmtt) REVERT: B 900 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8377 (mtm) REVERT: B 916 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8627 (tt) REVERT: C 32 PHE cc_start: 0.6627 (m-80) cc_final: 0.6382 (m-10) REVERT: C 84 LEU cc_start: 0.5285 (OUTLIER) cc_final: 0.5066 (mp) REVERT: C 86 PHE cc_start: 0.6064 (OUTLIER) cc_final: 0.5736 (t80) REVERT: C 306 PHE cc_start: 0.8056 (m-80) cc_final: 0.7747 (m-80) REVERT: H 11 LEU cc_start: 0.2887 (OUTLIER) cc_final: 0.2539 (mp) REVERT: H 82 LEU cc_start: 0.1229 (OUTLIER) cc_final: 0.0098 (mp) REVERT: H 104 TYR cc_start: 0.2438 (t80) cc_final: 0.2099 (m-80) REVERT: H 204 LEU cc_start: 0.1344 (mt) cc_final: 0.0700 (pt) REVERT: L 49 MET cc_start: 0.2085 (pmm) cc_final: -0.0650 (mtt) REVERT: L 108 LEU cc_start: -0.0012 (tp) cc_final: -0.0303 (pp) REVERT: L 140 LEU cc_start: 0.0743 (mp) cc_final: 0.0242 (tp) REVERT: J 198 THR cc_start: 0.1615 (p) cc_final: 0.1293 (t) REVERT: J 216 LYS cc_start: 0.1686 (OUTLIER) cc_final: 0.1319 (tptm) REVERT: N 49 MET cc_start: 0.1401 (OUTLIER) cc_final: -0.0875 (ttm) outliers start: 179 outliers final: 89 residues processed: 359 average time/residue: 1.0012 time to fit residues: 454.8627 Evaluate side-chains 282 residues out of total 3380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 178 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain N residue 199 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 310 optimal weight: 30.0000 chunk 211 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 277 optimal weight: 6.9990 chunk 153 optimal weight: 0.6980 chunk 318 optimal weight: 50.0000 chunk 257 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 334 optimal weight: 30.0000 chunk 94 optimal weight: 0.9980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 658 ASN B 703 ASN B1142 GLN C 540 ASN C 914 ASN C1005 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN N 199 GLN ** N 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 31691 Z= 0.291 Angle : 0.723 13.073 43136 Z= 0.357 Chirality : 0.051 0.728 5117 Planarity : 0.005 0.053 5460 Dihedral : 7.523 59.948 5644 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.93 % Favored : 92.81 % Rotamer: Outliers : 5.36 % Allowed : 24.44 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 3812 helix: 1.03 (0.21), residues: 688 sheet: -0.17 (0.15), residues: 1094 loop : -2.01 (0.12), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 114 HIS 0.004 0.001 HIS A1048 PHE 0.028 0.002 PHE B 168 TYR 0.022 0.002 TYR B 453 ARG 0.008 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 202 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0319 (mpp) cc_final: -0.1972 (ptp) REVERT: A 553 THR cc_start: 0.8305 (p) cc_final: 0.8075 (t) REVERT: A 673 SER cc_start: 0.8156 (OUTLIER) cc_final: 0.7653 (p) REVERT: A 692 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8478 (mm) REVERT: A 856 ASN cc_start: 0.7423 (OUTLIER) cc_final: 0.7131 (p0) REVERT: A 964 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7817 (mppt) REVERT: A 1010 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: B 52 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: B 129 LYS cc_start: 0.6548 (mtpt) cc_final: 0.5992 (mppt) REVERT: B 164 ASN cc_start: 0.5103 (OUTLIER) cc_final: 0.4740 (t0) REVERT: B 389 ASP cc_start: 0.6788 (OUTLIER) cc_final: 0.6410 (m-30) REVERT: B 414 GLN cc_start: 0.3190 (OUTLIER) cc_final: 0.1603 (mp10) REVERT: B 422 ASN cc_start: 0.5171 (OUTLIER) cc_final: 0.4883 (p0) REVERT: B 455 LEU cc_start: 0.2751 (OUTLIER) cc_final: 0.2388 (tp) REVERT: B 506 GLN cc_start: 0.6108 (OUTLIER) cc_final: 0.5902 (pt0) REVERT: B 528 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.6643 (mtpt) REVERT: B 900 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8375 (mtm) REVERT: B 916 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8703 (tt) REVERT: C 32 PHE cc_start: 0.6708 (m-80) cc_final: 0.6444 (m-10) REVERT: C 190 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.5864 (mtp85) REVERT: C 306 PHE cc_start: 0.8073 (m-80) cc_final: 0.7693 (m-80) REVERT: C 540 ASN cc_start: 0.6874 (m-40) cc_final: 0.6617 (m110) REVERT: H 11 LEU cc_start: 0.3054 (OUTLIER) cc_final: 0.2633 (mp) REVERT: H 82 LEU cc_start: 0.1133 (OUTLIER) cc_final: 0.0022 (mp) REVERT: H 104 TYR cc_start: 0.2543 (t80) cc_final: 0.2113 (m-80) REVERT: H 204 LEU cc_start: 0.1251 (mt) cc_final: 0.0659 (pt) REVERT: L 49 MET cc_start: 0.2057 (pmm) cc_final: -0.0768 (mtt) REVERT: L 108 LEU cc_start: 0.0404 (tp) cc_final: -0.0009 (pp) REVERT: L 140 LEU cc_start: 0.0162 (mp) cc_final: -0.0391 (tp) REVERT: L 199 GLN cc_start: 0.2633 (OUTLIER) cc_final: 0.2211 (mp-120) REVERT: J 216 LYS cc_start: 0.1778 (OUTLIER) cc_final: 0.1449 (tptm) REVERT: N 49 MET cc_start: 0.1546 (OUTLIER) cc_final: -0.0797 (ttm) outliers start: 181 outliers final: 89 residues processed: 359 average time/residue: 0.9355 time to fit residues: 426.0988 Evaluate side-chains 289 residues out of total 3380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 179 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain N residue 199 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 125 optimal weight: 10.0000 chunk 336 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 219 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 373 optimal weight: 10.0000 chunk 310 optimal weight: 0.2980 chunk 172 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 422 ASN A 856 ASN A 957 GLN B 506 GLN B 542 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C1005 GLN L 199 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN ** J 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31691 Z= 0.236 Angle : 0.692 12.897 43136 Z= 0.339 Chirality : 0.050 0.639 5117 Planarity : 0.004 0.053 5460 Dihedral : 7.318 59.680 5642 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.93 % Favored : 92.81 % Rotamer: Outliers : 5.18 % Allowed : 24.59 % Favored : 70.24 % 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: -1.12 (0.13), residues: 3812 helix: 1.17 (0.20), residues: 693 sheet: 0.04 (0.15), residues: 1078 loop : -1.95 (0.12), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 114 HIS 0.003 0.001 HIS A1048 PHE 0.030 0.002 PHE B 168 TYR 0.019 0.001 TYR A 170 ARG 0.007 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 190 time to evaluate : 3.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0486 (mpp) cc_final: -0.1916 (ptp) REVERT: A 692 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8520 (mm) REVERT: A 787 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7892 (mm-40) REVERT: A 856 ASN cc_start: 0.7399 (OUTLIER) cc_final: 0.7053 (p0) REVERT: A 964 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7775 (mppt) REVERT: B 129 LYS cc_start: 0.6642 (mtpt) cc_final: 0.6090 (mppt) REVERT: B 164 ASN cc_start: 0.4868 (OUTLIER) cc_final: 0.4487 (t0) REVERT: B 389 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6635 (m-30) REVERT: B 414 GLN cc_start: 0.3180 (OUTLIER) cc_final: 0.1548 (mp10) REVERT: B 455 LEU cc_start: 0.2670 (OUTLIER) cc_final: 0.2324 (tp) REVERT: B 517 LEU cc_start: 0.5467 (OUTLIER) cc_final: 0.4976 (mm) REVERT: B 528 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6805 (mtpt) REVERT: B 786 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7751 (mttt) REVERT: B 900 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8340 (mtm) REVERT: B 916 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8579 (tt) REVERT: C 32 PHE cc_start: 0.6688 (m-80) cc_final: 0.6410 (m-10) REVERT: C 190 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.5903 (mtp85) REVERT: C 306 PHE cc_start: 0.8009 (m-80) cc_final: 0.7618 (m-80) REVERT: C 585 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6318 (mt) REVERT: H 11 LEU cc_start: 0.3038 (OUTLIER) cc_final: 0.2578 (mp) REVERT: H 100 GLU cc_start: 0.3656 (OUTLIER) cc_final: 0.3359 (pt0) REVERT: H 204 LEU cc_start: 0.1258 (mt) cc_final: 0.0661 (pt) REVERT: L 49 MET cc_start: 0.1624 (pmm) cc_final: -0.0790 (mtt) REVERT: L 140 LEU cc_start: 0.0819 (OUTLIER) cc_final: 0.0249 (pp) REVERT: J 216 LYS cc_start: 0.1759 (OUTLIER) cc_final: 0.1435 (tptm) REVERT: N 49 MET cc_start: 0.1549 (OUTLIER) cc_final: -0.0797 (ttm) REVERT: N 99 LEU cc_start: 0.0432 (OUTLIER) cc_final: -0.0250 (tp) outliers start: 175 outliers final: 96 residues processed: 345 average time/residue: 0.9269 time to fit residues: 410.0093 Evaluate side-chains 285 residues out of total 3380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 168 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain N residue 197 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.3164 > 50: distance: 19 - 66: 15.797 distance: 35 - 39: 9.730 distance: 39 - 40: 10.363 distance: 39 - 159: 11.982 distance: 40 - 41: 18.874 distance: 40 - 43: 8.383 distance: 41 - 42: 10.324 distance: 41 - 47: 15.996 distance: 43 - 44: 14.113 distance: 43 - 45: 16.145 distance: 44 - 46: 14.691 distance: 47 - 48: 24.438 distance: 48 - 49: 4.571 distance: 48 - 51: 4.656 distance: 49 - 50: 3.606 distance: 51 - 52: 9.295 distance: 53 - 54: 4.862 distance: 54 - 55: 11.339 distance: 54 - 57: 7.504 distance: 55 - 56: 7.994 distance: 55 - 61: 12.919 distance: 57 - 58: 21.506 distance: 58 - 59: 6.502 distance: 58 - 60: 10.658 distance: 61 - 62: 13.472 distance: 62 - 63: 13.807 distance: 62 - 65: 18.796 distance: 63 - 64: 10.547 distance: 63 - 67: 14.312 distance: 65 - 66: 28.109 distance: 67 - 68: 11.163 distance: 68 - 69: 4.109 distance: 68 - 71: 11.346 distance: 69 - 70: 6.319 distance: 69 - 74: 30.366 distance: 71 - 73: 15.443 distance: 74 - 75: 17.485 distance: 75 - 76: 16.020 distance: 75 - 78: 13.789 distance: 76 - 77: 18.391 distance: 76 - 79: 12.785 distance: 79 - 80: 9.279 distance: 80 - 81: 27.499 distance: 80 - 83: 15.064 distance: 81 - 82: 20.376 distance: 81 - 87: 29.056 distance: 83 - 84: 6.200 distance: 84 - 85: 19.780 distance: 84 - 86: 14.769 distance: 87 - 88: 22.621 distance: 88 - 89: 12.447 distance: 88 - 91: 14.768 distance: 89 - 90: 4.331 distance: 89 - 99: 7.101 distance: 90 - 120: 20.934 distance: 91 - 92: 11.833 distance: 92 - 93: 7.346 distance: 92 - 94: 11.285 distance: 93 - 95: 18.580 distance: 94 - 96: 16.493 distance: 95 - 97: 7.289 distance: 96 - 97: 4.753 distance: 97 - 98: 12.820 distance: 99 - 100: 17.578 distance: 100 - 101: 14.712 distance: 100 - 103: 26.360 distance: 101 - 102: 14.083 distance: 101 - 105: 11.005 distance: 102 - 126: 15.487 distance: 103 - 104: 4.508 distance: 105 - 106: 6.923 distance: 106 - 107: 3.531 distance: 106 - 109: 9.806 distance: 107 - 108: 6.352 distance: 107 - 112: 3.551 distance: 109 - 110: 15.576 distance: 109 - 111: 8.329