Starting phenix.real_space_refine on Thu Feb 22 16:36:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czz_30522/02_2024/7czz_30522.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czz_30522/02_2024/7czz_30522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czz_30522/02_2024/7czz_30522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czz_30522/02_2024/7czz_30522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czz_30522/02_2024/7czz_30522.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czz_30522/02_2024/7czz_30522.pdb" } resolution = 3.2 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 22020 2.51 5 N 5682 2.21 5 O 6919 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 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 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 154": "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 ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 554": "OE1" <-> "OE2" 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 154": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 "K GLU 17": "OE1" <-> "OE2" Residue "K GLU 171": "OE1" <-> "OE2" Residue "K PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M GLU 171": "OE1" <-> "OE2" Residue "M PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N GLU 171": "OE1" <-> "OE2" Residue "N PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34771 Number of models: 1 Model: "" Number of chains: 37 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: 7870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7870 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 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: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "K" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1685 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "M" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1685 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "N" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1685 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "c" 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: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 17.34, per 1000 atoms: 0.50 Number of scatterers: 34771 At special positions: 0 Unit cell: (154.354, 176.094, 246.749, 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 150 16.00 O 6919 8.00 N 5682 7.00 C 22020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.27 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=2.15 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.14 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.38 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.15 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.08 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 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=2.26 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=2.15 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=2.10 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=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 94 " distance=2.80 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 200 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 149 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 94 " distance=2.80 Simple disulfide: pdb=" SG CYS M 140 " - pdb=" SG CYS M 200 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 149 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 94 " distance=2.80 Simple disulfide: pdb=" SG CYS N 140 " - pdb=" SG CYS N 200 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B1409 " - " NAG B1410 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " NAG f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " NAG g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " NAG h 3 " 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 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " 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 L 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 331 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 709 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 331 " " NAG Y 1 " - " ASN C 343 " " NAG Z 1 " - " ASN C 709 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 801 " " NAG c 1 " - " ASN C1074 " " NAG d 1 " - " ASN C1098 " " NAG e 1 " - " ASN C1134 " " NAG f 1 " - " ASN H 73 " " NAG g 1 " - " ASN I 73 " " NAG h 1 " - " ASN J 73 " Time building additional restraints: 13.91 Conformation dependent library (CDL) restraints added in 5.9 seconds 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8120 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 76 sheets defined 17.9% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A 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: 3.626A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.632A 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: 3.654A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.521A 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: 3.636A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.539A 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: 3.646A 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: 3.994A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.627A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.678A 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: 3.650A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A 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 982 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 993 through 1033 removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.626A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 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: 3.963A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.638A 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: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.012A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.371A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.119A 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: 3.505A 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: 4.073A 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: 3.686A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.626A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.584A 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: 3.718A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.603A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.636A 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: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.356A 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: 3.553A 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: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.817A 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: 3.537A 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 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'K' and resid 127 through 134 Processing helix chain 'K' and resid 189 through 193 Processing helix chain 'I' and resid 196 through 198 No H-bonds generated for 'chain 'I' and resid 196 through 198' Processing helix chain 'M' and resid 127 through 134 Processing helix chain 'M' and resid 189 through 193 Processing helix chain 'J' and resid 196 through 198 No H-bonds generated for 'chain 'J' and resid 196 through 198' Processing helix chain 'N' and resid 127 through 134 Processing helix chain 'N' and resid 189 through 193 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.682A 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: 4.436A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.949A 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: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.045A 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: 6.680A 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: 3.547A 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: 4.621A 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: 3.542A 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: 4.785A 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: 5.336A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.254A 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: 6.417A 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: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A 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: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A 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: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A 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: 4.506A 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: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.610A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 92 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.516A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 166 through 170 removed outlier: 4.821A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.572A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.654A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.219A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.214A 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: 4.596A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, 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=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.557A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.534A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 132 through 135 removed outlier: 4.138A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 193 through 194 removed outlier: 5.991A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 275 through 279 removed outlier: 3.887A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.118A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.532A 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: 6.705A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.708A 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=AE5, 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=AE6, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.605A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A 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: 6.693A 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: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A 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: 6.693A 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: 6.148A 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: 3.879A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.567A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.995A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.576A pdb=" N TYR H 94 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 129 through 133 removed outlier: 5.009A pdb=" N ALA H 146 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 193 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 148 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 191 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 150 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 189 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 152 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 187 " --> pdb=" O LYS H 152 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 129 through 133 removed outlier: 5.009A pdb=" N ALA H 146 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 193 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 148 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 191 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 150 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 189 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 152 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 187 " --> pdb=" O LYS H 152 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 159 through 163 Processing sheet with id=AG1, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.913A pdb=" N THR K 5 " --> pdb=" O LYS K 24 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS K 24 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS K 23 " --> pdb=" O PHE K 77 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE K 77 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 42 through 44 Processing sheet with id=AG3, first strand: chain 'K' and resid 120 through 124 Processing sheet with id=AG4, first strand: chain 'K' and resid 159 through 160 Processing sheet with id=AG5, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.995A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER I 7 " --> pdb=" O SER I 21 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.575A pdb=" N TYR I 94 " --> pdb=" O THR I 116 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA I 146 " --> pdb=" O VAL I 193 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL I 193 " --> pdb=" O ALA I 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 148 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL I 191 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 150 " --> pdb=" O SER I 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 189 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS I 152 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 187 " --> pdb=" O LYS I 152 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA I 146 " --> pdb=" O VAL I 193 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL I 193 " --> pdb=" O ALA I 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 148 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL I 191 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 150 " --> pdb=" O SER I 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 189 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS I 152 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 187 " --> pdb=" O LYS I 152 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 159 through 163 Processing sheet with id=AH1, first strand: chain 'M' and resid 5 through 6 removed outlier: 3.914A pdb=" N THR M 5 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS M 24 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS M 23 " --> pdb=" O PHE M 77 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE M 77 " --> pdb=" O CYS M 23 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 42 through 44 Processing sheet with id=AH3, first strand: chain 'M' and resid 120 through 124 Processing sheet with id=AH4, first strand: chain 'M' and resid 159 through 160 Processing sheet with id=AH5, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.996A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER J 7 " --> pdb=" O SER J 21 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.575A pdb=" N TYR J 94 " --> pdb=" O THR J 116 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA J 146 " --> pdb=" O VAL J 193 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL J 193 " --> pdb=" O ALA J 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 148 " --> pdb=" O VAL J 191 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL J 191 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU J 150 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 189 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS J 152 " --> pdb=" O LEU J 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 187 " --> pdb=" O LYS J 152 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA J 146 " --> pdb=" O VAL J 193 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL J 193 " --> pdb=" O ALA J 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 148 " --> pdb=" O VAL J 191 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL J 191 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU J 150 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 189 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS J 152 " --> pdb=" O LEU J 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 187 " --> pdb=" O LYS J 152 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 159 through 163 Processing sheet with id=AI1, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.914A pdb=" N THR N 5 " --> pdb=" O LYS N 24 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS N 24 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS N 23 " --> pdb=" O PHE N 77 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE N 77 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'N' and resid 42 through 44 Processing sheet with id=AI3, first strand: chain 'N' and resid 120 through 124 Processing sheet with id=AI4, first strand: chain 'N' and resid 159 through 160 1145 hydrogen bonds defined for protein. 3057 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.25 Time building geometry restraints manager: 15.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5784 1.31 - 1.45: 10449 1.45 - 1.58: 19100 1.58 - 1.71: 3 1.71 - 1.85: 192 Bond restraints: 35528 Sorted by residual: bond pdb=" CA GLN C 239 " pdb=" C GLN C 239 " ideal model delta sigma weight residual 1.525 1.420 0.105 1.11e-02 8.12e+03 9.03e+01 bond pdb=" CA HIS B 49 " pdb=" C HIS B 49 " ideal model delta sigma weight residual 1.520 1.405 0.116 1.22e-02 6.72e+03 8.99e+01 bond pdb=" CA ASN C 30 " pdb=" C ASN C 30 " ideal model delta sigma weight residual 1.520 1.416 0.104 1.16e-02 7.43e+03 8.07e+01 bond pdb=" CA ARG C 44 " pdb=" C ARG C 44 " ideal model delta sigma weight residual 1.521 1.415 0.106 1.24e-02 6.50e+03 7.37e+01 bond pdb=" CA TYR B 204 " pdb=" C TYR B 204 " ideal model delta sigma weight residual 1.523 1.422 0.101 1.18e-02 7.18e+03 7.30e+01 ... (remaining 35523 not shown) Histogram of bond angle deviations from ideal: 96.93 - 105.24: 837 105.24 - 113.55: 20008 113.55 - 121.87: 20037 121.87 - 130.18: 7309 130.18 - 138.49: 148 Bond angle restraints: 48339 Sorted by residual: angle pdb=" CA PHE C 32 " pdb=" CB PHE C 32 " pdb=" CG PHE C 32 " ideal model delta sigma weight residual 113.80 103.52 10.28 1.00e+00 1.00e+00 1.06e+02 angle pdb=" CA GLN C 271 " pdb=" C GLN C 271 " pdb=" N PRO C 272 " ideal model delta sigma weight residual 117.82 125.27 -7.45 7.80e-01 1.64e+00 9.11e+01 angle pdb=" CA GLU C 224 " pdb=" C GLU C 224 " pdb=" O GLU C 224 " ideal model delta sigma weight residual 120.19 112.57 7.62 8.40e-01 1.42e+00 8.23e+01 angle pdb=" CA ASN B 188 " pdb=" CB ASN B 188 " pdb=" CG ASN B 188 " ideal model delta sigma weight residual 112.60 103.62 8.98 1.00e+00 1.00e+00 8.06e+01 angle pdb=" CA PHE C 238 " pdb=" CB PHE C 238 " pdb=" CG PHE C 238 " ideal model delta sigma weight residual 113.80 122.42 -8.62 1.00e+00 1.00e+00 7.43e+01 ... (remaining 48334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 19170 17.92 - 35.83: 2118 35.83 - 53.75: 687 53.75 - 71.67: 209 71.67 - 89.59: 62 Dihedral angle restraints: 22246 sinusoidal: 9612 harmonic: 12634 Sorted by residual: 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 21.05 71.95 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual 93.00 35.72 57.28 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" N ASP B 198 " pdb=" C ASP B 198 " pdb=" CA ASP B 198 " pdb=" CB ASP B 198 " ideal model delta harmonic sigma weight residual 122.80 138.69 -15.89 0 2.50e+00 1.60e-01 4.04e+01 ... (remaining 22243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5684 0.328 - 0.657: 30 0.657 - 0.985: 6 0.985 - 1.313: 1 1.313 - 1.642: 3 Chirality restraints: 5724 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-02 2.50e+03 6.61e+03 chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " 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 D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-02 2.50e+03 2.56e+02 ... (remaining 5721 not shown) Planarity restraints: 6179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 282 " 0.243 2.00e-02 2.50e+03 3.37e-01 1.42e+03 pdb=" CG ASN B 282 " -0.115 2.00e-02 2.50e+03 pdb=" OD1 ASN B 282 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 282 " -0.561 2.00e-02 2.50e+03 pdb=" C1 NAG B1405 " 0.424 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 2 " 0.352 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG Q 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG Q 2 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG Q 2 " -0.535 2.00e-02 2.50e+03 pdb=" O7 NAG Q 2 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 2 " -0.295 2.00e-02 2.50e+03 2.48e-01 7.68e+02 pdb=" C7 NAG f 2 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG f 2 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG f 2 " 0.423 2.00e-02 2.50e+03 pdb=" O7 NAG f 2 " -0.017 2.00e-02 2.50e+03 ... (remaining 6176 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 391 2.47 - 3.08: 24676 3.08 - 3.69: 50073 3.69 - 4.29: 76148 4.29 - 4.90: 125450 Nonbonded interactions: 276738 Sorted by model distance: nonbonded pdb=" O ALA K 86 " pdb=" OE1 GLU K 87 " model vdw 1.865 3.040 nonbonded pdb=" O ALA M 86 " pdb=" OE1 GLU M 87 " model vdw 1.865 3.040 nonbonded pdb=" O ALA N 86 " pdb=" OE1 GLU N 87 " model vdw 1.865 3.040 nonbonded pdb=" O ARG C 273 " pdb=" OG1 THR C 274 " model vdw 1.914 2.440 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.980 2.520 ... (remaining 276733 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 620 or resid 641 through 939 or resid 944 throu \ gh 1146 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 826 or resid 855 through 1146 or resid 1401 thr \ ough 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'f' selection = chain 'g' selection = chain 'h' } 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: 1.190 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: 7.360 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 89.710 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.690 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 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 : 0.012 0.118 35528 Z= 0.805 Angle : 1.283 13.492 48339 Z= 0.774 Chirality : 0.088 1.642 5724 Planarity : 0.012 0.302 6128 Dihedral : 17.639 89.587 13973 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 40.65 Ramachandran Plot: Outliers : 4.97 % Allowed : 11.72 % Favored : 83.31 % Rotamer: Outliers : 12.78 % Allowed : 17.52 % Favored : 69.69 % Cbeta Deviations : 0.20 % 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: -3.98 (0.11), residues: 4283 helix: -2.26 (0.16), residues: 683 sheet: -1.54 (0.14), residues: 1149 loop : -3.48 (0.10), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.166 0.004 TRP C 64 HIS 0.009 0.002 HIS B 207 PHE 0.119 0.005 PHE C 220 TYR 0.091 0.003 TYR C 38 ARG 0.013 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 483 poor density : 484 time to evaluate : 3.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ILE cc_start: 0.5167 (OUTLIER) cc_final: 0.4741 (mt) REVERT: A 459 SER cc_start: 0.4454 (OUTLIER) cc_final: 0.4035 (m) REVERT: A 486 PHE cc_start: 0.1855 (OUTLIER) cc_final: 0.1309 (p90) REVERT: A 746 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8502 (p) REVERT: A 878 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8978 (tt) REVERT: A 998 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8605 (m) REVERT: B 34 ARG cc_start: 0.5764 (OUTLIER) cc_final: 0.5512 (mtp85) REVERT: B 157 PHE cc_start: 0.4068 (OUTLIER) cc_final: 0.3743 (t80) REVERT: B 190 ARG cc_start: 0.5893 (OUTLIER) cc_final: 0.4895 (ptp90) REVERT: B 640 SER cc_start: 0.5078 (OUTLIER) cc_final: 0.4046 (m) REVERT: B 787 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8048 (mt0) REVERT: C 878 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8738 (tt) REVERT: H 31 SER cc_start: 0.1000 (p) cc_final: 0.0720 (t) REVERT: H 165 SER cc_start: 0.3475 (OUTLIER) cc_final: 0.2717 (t) REVERT: H 174 THR cc_start: 0.3878 (t) cc_final: 0.3571 (m) REVERT: K 59 THR cc_start: 0.4174 (OUTLIER) cc_final: 0.3959 (p) REVERT: I 30 THR cc_start: 0.3042 (OUTLIER) cc_final: 0.2800 (p) REVERT: I 48 MET cc_start: -0.0612 (OUTLIER) cc_final: -0.0897 (ptm) REVERT: I 165 SER cc_start: 0.0512 (OUTLIER) cc_final: 0.0144 (p) REVERT: M 97 TYR cc_start: 0.2509 (OUTLIER) cc_final: 0.1976 (m-10) REVERT: J 33 ASP cc_start: 0.1145 (OUTLIER) cc_final: 0.0553 (p0) REVERT: J 103 VAL cc_start: 0.0870 (OUTLIER) cc_final: 0.0521 (t) REVERT: N 4 MET cc_start: 0.1177 (mmm) cc_final: 0.0913 (ttt) REVERT: N 6 GLN cc_start: 0.1742 (OUTLIER) cc_final: 0.1173 (mm110) outliers start: 483 outliers final: 125 residues processed: 891 average time/residue: 0.4393 time to fit residues: 647.6340 Evaluate side-chains 379 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 233 time to evaluate : 3.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 212 SER Chi-restraints excluded: chain K residue 31 TYR Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain M residue 38 TYR Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 97 TYR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 50 TRP Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 38 TYR Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 177 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 7.9990 chunk 327 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 220 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 338 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 chunk 392 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 81 ASN A 134 GLN A 137 ASN A 188 ASN A 314 GLN A 394 ASN A 422 ASN A 440 ASN A 481 ASN A 498 GLN A 540 ASN A 613 GLN A 644 GLN A 690 GLN A 703 ASN A 787 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 969 ASN A 992 GLN A1002 GLN B 81 ASN B 87 ASN B 115 GLN B 394 ASN B 422 ASN B 440 ASN B 481 ASN B 498 GLN B 580 GLN B 607 GLN B 804 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1005 GLN B1054 GLN C 30 ASN C 66 HIS C 87 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 394 ASN C 422 ASN C 440 ASN C 481 ASN C 498 GLN C 641 ASN C 655 HIS C 703 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 969 ASN C 992 GLN C1005 GLN C1010 GLN C1071 GLN C1101 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN ** N 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 GLN ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 35528 Z= 0.279 Angle : 0.829 11.642 48339 Z= 0.416 Chirality : 0.053 0.569 5724 Planarity : 0.005 0.072 6128 Dihedral : 10.257 69.200 6559 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.88 % Favored : 89.19 % Rotamer: Outliers : 6.06 % Allowed : 19.19 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.12), residues: 4283 helix: -0.18 (0.19), residues: 693 sheet: -0.86 (0.14), residues: 1207 loop : -2.95 (0.11), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 47 HIS 0.007 0.001 HIS B 519 PHE 0.026 0.002 PHE I 175 TYR 0.027 0.002 TYR B 28 ARG 0.007 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 273 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8085 (t) cc_final: 0.7879 (m) REVERT: A 365 TYR cc_start: 0.5093 (m-80) cc_final: 0.4329 (m-10) REVERT: A 646 ARG cc_start: 0.7497 (tpm170) cc_final: 0.6954 (tpt90) REVERT: A 856 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8183 (p0) REVERT: A 878 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8879 (tt) REVERT: B 153 MET cc_start: 0.2417 (tpp) cc_final: 0.1668 (ttt) REVERT: C 878 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8646 (tt) REVERT: I 70 MET cc_start: 0.1089 (tmm) cc_final: 0.0429 (tmm) REVERT: I 81 MET cc_start: 0.2946 (mmm) cc_final: 0.0461 (ttp) REVERT: I 107 LYS cc_start: 0.1254 (OUTLIER) cc_final: 0.0806 (mmmm) REVERT: I 118 VAL cc_start: -0.0871 (OUTLIER) cc_final: -0.1097 (t) REVERT: I 187 LEU cc_start: 0.1995 (OUTLIER) cc_final: 0.1256 (tp) REVERT: M 4 MET cc_start: -0.0146 (mmt) cc_final: -0.0694 (mmm) REVERT: J 33 ASP cc_start: 0.0897 (OUTLIER) cc_final: 0.0124 (p0) REVERT: N 4 MET cc_start: 0.1399 (mmm) cc_final: 0.0877 (ttt) REVERT: N 179 TYR cc_start: 0.2735 (OUTLIER) cc_final: 0.2413 (m-80) outliers start: 229 outliers final: 115 residues processed: 473 average time/residue: 0.4228 time to fit residues: 340.7874 Evaluate side-chains 335 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 212 time to evaluate : 3.611 ------------------------------------------------------------------------------- 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 155 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER 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 569 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 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 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP 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 1132 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 122 PHE Chi-restraints excluded: chain K residue 137 SER Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 31 TYR Chi-restraints excluded: chain N residue 38 TYR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 122 PHE Chi-restraints excluded: chain N residue 179 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 326 optimal weight: 20.0000 chunk 267 optimal weight: 4.9990 chunk 108 optimal weight: 0.0670 chunk 393 optimal weight: 20.0000 chunk 424 optimal weight: 9.9990 chunk 350 optimal weight: 6.9990 chunk 389 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 315 optimal weight: 9.9990 overall best weight: 4.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 239 GLN A 360 ASN A 613 GLN A 824 ASN A 856 ASN A 935 GLN A 955 ASN B 30 ASN B 125 ASN B 245 HIS B 690 GLN B 935 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 207 HIS C 394 ASN C 450 ASN C 606 ASN C 804 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 GLN K 166 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 35528 Z= 0.437 Angle : 0.840 14.381 48339 Z= 0.417 Chirality : 0.054 0.418 5724 Planarity : 0.006 0.062 6128 Dihedral : 9.166 59.942 6408 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.85 % Favored : 89.47 % Rotamer: Outliers : 6.67 % Allowed : 19.35 % Favored : 73.98 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.12), residues: 4283 helix: 0.26 (0.20), residues: 694 sheet: -0.59 (0.14), residues: 1217 loop : -2.62 (0.11), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 56 HIS 0.007 0.002 HIS B 207 PHE 0.021 0.002 PHE C1103 TYR 0.028 0.002 TYR M 38 ARG 0.006 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 238 time to evaluate : 3.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.6414 (mm) cc_final: 0.6210 (mp) REVERT: A 169 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6543 (tt0) REVERT: A 347 PHE cc_start: 0.4887 (OUTLIER) cc_final: 0.4532 (m-10) REVERT: A 509 ARG cc_start: 0.4157 (OUTLIER) cc_final: 0.3276 (mtm-85) REVERT: A 525 CYS cc_start: 0.5008 (OUTLIER) cc_final: 0.4730 (m) REVERT: A 646 ARG cc_start: 0.7494 (tpm170) cc_final: 0.7223 (tpt90) REVERT: B 97 LYS cc_start: 0.6195 (OUTLIER) cc_final: 0.5607 (mttm) REVERT: B 469 SER cc_start: 0.1430 (OUTLIER) cc_final: 0.1004 (t) REVERT: B 740 MET cc_start: 0.8365 (ttt) cc_final: 0.8024 (ttt) REVERT: C 215 ASP cc_start: 0.1539 (OUTLIER) cc_final: 0.0851 (m-30) REVERT: C 585 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7604 (mt) REVERT: C 770 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8706 (pt) REVERT: K 4 MET cc_start: 0.1019 (tpt) cc_final: 0.0494 (tpp) REVERT: I 23 LYS cc_start: 0.3472 (tptt) cc_final: 0.3185 (mttp) REVERT: I 81 MET cc_start: 0.3044 (mmm) cc_final: 0.2144 (mmt) REVERT: I 187 LEU cc_start: 0.1787 (OUTLIER) cc_final: 0.1020 (tp) REVERT: I 215 LYS cc_start: 0.2139 (tppt) cc_final: 0.1884 (tptm) REVERT: M 4 MET cc_start: -0.0198 (mmt) cc_final: -0.0785 (mmm) REVERT: N 4 MET cc_start: 0.1727 (mmm) cc_final: 0.1387 (ttp) REVERT: N 31 TYR cc_start: 0.2204 (OUTLIER) cc_final: 0.1833 (t80) REVERT: N 179 TYR cc_start: 0.2932 (OUTLIER) cc_final: 0.2433 (m-80) outliers start: 252 outliers final: 148 residues processed: 455 average time/residue: 0.4212 time to fit residues: 330.4803 Evaluate side-chains 358 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 198 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1017 GLU 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 1132 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 31 TYR Chi-restraints excluded: chain N residue 38 TYR Chi-restraints excluded: chain N residue 122 PHE Chi-restraints excluded: chain N residue 179 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 40.0000 chunk 295 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 187 optimal weight: 0.9990 chunk 263 optimal weight: 3.9990 chunk 394 optimal weight: 30.0000 chunk 417 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 373 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 115 GLN A 856 ASN A 935 GLN A 955 ASN B 245 HIS B 422 ASN B 450 ASN B 762 GLN B 804 GLN B 935 GLN B 957 GLN C 81 ASN C 207 HIS C 394 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 143 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 35528 Z= 0.308 Angle : 0.730 10.603 48339 Z= 0.360 Chirality : 0.049 0.536 5724 Planarity : 0.005 0.055 6128 Dihedral : 8.518 59.729 6390 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.64 % Favored : 90.73 % Rotamer: Outliers : 5.48 % Allowed : 21.12 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.12), residues: 4283 helix: 0.66 (0.20), residues: 688 sheet: -0.32 (0.14), residues: 1213 loop : -2.41 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 56 HIS 0.017 0.001 HIS B 245 PHE 0.027 0.002 PHE B 133 TYR 0.021 0.002 TYR C 170 ARG 0.004 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 230 time to evaluate : 3.956 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 169 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6844 (mt-10) REVERT: A 347 PHE cc_start: 0.4891 (OUTLIER) cc_final: 0.4620 (m-10) REVERT: A 509 ARG cc_start: 0.3966 (OUTLIER) cc_final: 0.2966 (mtm-85) REVERT: A 525 CYS cc_start: 0.4975 (OUTLIER) cc_final: 0.4585 (m) REVERT: A 787 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: B 469 SER cc_start: 0.1851 (OUTLIER) cc_final: 0.1496 (t) REVERT: B 569 ILE cc_start: 0.7588 (mp) cc_final: 0.7177 (mp) REVERT: B 740 MET cc_start: 0.8367 (ttt) cc_final: 0.8030 (ttt) REVERT: C 215 ASP cc_start: 0.1402 (OUTLIER) cc_final: 0.0815 (m-30) REVERT: C 239 GLN cc_start: 0.7112 (tm-30) cc_final: 0.6795 (tm-30) REVERT: C 770 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8693 (pt) REVERT: H 182 SER cc_start: -0.1005 (OUTLIER) cc_final: -0.1229 (t) REVERT: H 198 LEU cc_start: -0.0091 (mt) cc_final: -0.0309 (pt) REVERT: I 23 LYS cc_start: 0.3640 (tptt) cc_final: 0.3334 (mttp) REVERT: I 81 MET cc_start: 0.3188 (mmm) cc_final: 0.2210 (mmt) REVERT: I 118 VAL cc_start: -0.1190 (OUTLIER) cc_final: -0.1417 (t) REVERT: I 187 LEU cc_start: 0.1597 (OUTLIER) cc_final: 0.0912 (tp) REVERT: I 215 LYS cc_start: 0.2522 (tppt) cc_final: 0.2137 (tptm) REVERT: M 4 MET cc_start: -0.0217 (mmt) cc_final: -0.0868 (mmm) REVERT: N 4 MET cc_start: 0.2041 (mmm) cc_final: 0.1652 (ttp) REVERT: N 111 GLU cc_start: 0.3213 (OUTLIER) cc_final: 0.2447 (tm-30) REVERT: N 179 TYR cc_start: 0.2698 (OUTLIER) cc_final: 0.2227 (m-80) outliers start: 207 outliers final: 135 residues processed: 407 average time/residue: 0.4244 time to fit residues: 297.1750 Evaluate side-chains 345 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 197 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1017 GLU 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 1132 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 31 TYR Chi-restraints excluded: chain N residue 38 TYR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 179 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 6.9990 chunk 237 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 356 optimal weight: 30.0000 chunk 288 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 374 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 957 GLN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 125 ASN C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 143 ASN M 166 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 35528 Z= 0.386 Angle : 0.762 11.898 48339 Z= 0.379 Chirality : 0.051 0.609 5724 Planarity : 0.005 0.056 6128 Dihedral : 8.423 59.609 6385 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.76 % Favored : 89.70 % Rotamer: Outliers : 6.19 % Allowed : 21.18 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.12), residues: 4283 helix: 0.56 (0.20), residues: 697 sheet: -0.25 (0.14), residues: 1234 loop : -2.32 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 36 HIS 0.008 0.002 HIS B1048 PHE 0.028 0.002 PHE M 122 TYR 0.024 0.002 TYR B 451 ARG 0.013 0.001 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 217 time to evaluate : 3.693 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 169 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6453 (tt0) REVERT: A 347 PHE cc_start: 0.4701 (OUTLIER) cc_final: 0.4465 (m-10) REVERT: A 509 ARG cc_start: 0.4126 (OUTLIER) cc_final: 0.2905 (mtm-85) REVERT: A 787 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8008 (mt0) REVERT: A 1034 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8999 (mt) REVERT: B 469 SER cc_start: 0.2182 (OUTLIER) cc_final: 0.1775 (t) REVERT: B 740 MET cc_start: 0.8357 (ttt) cc_final: 0.8045 (ttt) REVERT: C 215 ASP cc_start: 0.1438 (OUTLIER) cc_final: 0.0683 (m-30) REVERT: C 239 GLN cc_start: 0.6971 (tm-30) cc_final: 0.6728 (tm-30) REVERT: C 585 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7943 (mt) REVERT: C 770 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8704 (pt) REVERT: H 182 SER cc_start: -0.0051 (OUTLIER) cc_final: -0.0293 (t) REVERT: I 23 LYS cc_start: 0.3550 (tptt) cc_final: 0.3260 (mttp) REVERT: I 81 MET cc_start: 0.3313 (mmm) cc_final: 0.3026 (mmm) REVERT: I 112 TRP cc_start: 0.2929 (OUTLIER) cc_final: 0.2177 (t-100) REVERT: I 118 VAL cc_start: -0.1118 (OUTLIER) cc_final: -0.1361 (t) REVERT: I 139 SER cc_start: -0.4009 (OUTLIER) cc_final: -0.4375 (m) REVERT: I 187 LEU cc_start: 0.1652 (OUTLIER) cc_final: 0.0928 (tp) REVERT: I 215 LYS cc_start: 0.2440 (tppt) cc_final: 0.1999 (tptm) REVERT: M 4 MET cc_start: 0.0072 (mmt) cc_final: -0.0644 (mmm) REVERT: M 143 ASN cc_start: 0.1135 (OUTLIER) cc_final: 0.0663 (m110) REVERT: J 210 LYS cc_start: 0.1733 (OUTLIER) cc_final: 0.1188 (mtpp) REVERT: N 4 MET cc_start: 0.2029 (mmm) cc_final: 0.1552 (ttp) REVERT: N 111 GLU cc_start: 0.3248 (OUTLIER) cc_final: 0.2434 (tm-30) REVERT: N 179 TYR cc_start: 0.2779 (OUTLIER) cc_final: 0.2308 (m-80) outliers start: 234 outliers final: 166 residues processed: 423 average time/residue: 0.4226 time to fit residues: 310.1508 Evaluate side-chains 375 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 191 time to evaluate : 3.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN 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 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1017 GLU 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 1132 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 143 ASN Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 38 TYR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 179 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 8.9990 chunk 376 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 417 optimal weight: 6.9990 chunk 346 optimal weight: 30.0000 chunk 193 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 219 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 207 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 ASN K 35 ASN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 143 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 35528 Z= 0.305 Angle : 0.709 10.302 48339 Z= 0.351 Chirality : 0.048 0.513 5724 Planarity : 0.005 0.055 6128 Dihedral : 8.157 59.905 6378 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.85 % Favored : 90.64 % Rotamer: Outliers : 5.64 % Allowed : 21.73 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.12), residues: 4283 helix: 0.74 (0.20), residues: 691 sheet: -0.11 (0.14), residues: 1203 loop : -2.27 (0.12), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 56 HIS 0.006 0.001 HIS B1048 PHE 0.017 0.002 PHE A 86 TYR 0.019 0.001 TYR A 451 ARG 0.003 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 206 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 ARG cc_start: 0.4094 (OUTLIER) cc_final: 0.2772 (mtm-85) REVERT: A 787 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: B 569 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7086 (mp) REVERT: B 740 MET cc_start: 0.8335 (ttt) cc_final: 0.8019 (ttt) REVERT: C 215 ASP cc_start: 0.1403 (OUTLIER) cc_final: 0.0647 (m-30) REVERT: C 351 TYR cc_start: 0.3317 (OUTLIER) cc_final: 0.2653 (p90) REVERT: C 585 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7949 (mt) REVERT: C 770 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8690 (pt) REVERT: H 182 SER cc_start: -0.0031 (OUTLIER) cc_final: -0.0266 (t) REVERT: K 24 LYS cc_start: 0.2990 (OUTLIER) cc_final: 0.2758 (ptpt) REVERT: I 23 LYS cc_start: 0.3581 (tptt) cc_final: 0.3284 (mttp) REVERT: I 81 MET cc_start: 0.3318 (mmm) cc_final: 0.3064 (mmm) REVERT: I 118 VAL cc_start: -0.1131 (OUTLIER) cc_final: -0.1377 (t) REVERT: I 187 LEU cc_start: 0.1576 (OUTLIER) cc_final: 0.0811 (tp) REVERT: I 215 LYS cc_start: 0.2496 (tppt) cc_final: 0.2065 (tptm) REVERT: M 4 MET cc_start: 0.0061 (mmt) cc_final: -0.1124 (ttm) REVERT: N 111 GLU cc_start: 0.2912 (OUTLIER) cc_final: 0.2062 (tm-30) outliers start: 213 outliers final: 170 residues processed: 392 average time/residue: 0.4099 time to fit residues: 278.8678 Evaluate side-chains 369 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 187 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1017 GLU 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 1132 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 24 LYS Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 38 TYR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 30.0000 chunk 47 optimal weight: 7.9990 chunk 238 optimal weight: 0.8980 chunk 305 optimal weight: 1.9990 chunk 236 optimal weight: 8.9990 chunk 351 optimal weight: 30.0000 chunk 233 optimal weight: 0.5980 chunk 416 optimal weight: 0.9980 chunk 260 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 955 ASN A 969 ASN B 755 GLN B 856 ASN B 935 GLN C 207 HIS C 542 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35528 Z= 0.178 Angle : 0.646 10.811 48339 Z= 0.318 Chirality : 0.047 0.768 5724 Planarity : 0.004 0.056 6128 Dihedral : 7.577 58.915 6374 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.57 % Favored : 90.96 % Rotamer: Outliers : 4.47 % Allowed : 22.95 % Favored : 72.58 % 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: -1.30 (0.13), residues: 4283 helix: 1.13 (0.21), residues: 691 sheet: 0.15 (0.14), residues: 1218 loop : -2.15 (0.12), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 56 HIS 0.004 0.001 HIS B 207 PHE 0.015 0.001 PHE A 86 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 213 time to evaluate : 4.138 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 787 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: A 882 ILE cc_start: 0.9157 (mt) cc_final: 0.8952 (mt) REVERT: B 740 MET cc_start: 0.8297 (ttt) cc_final: 0.7940 (ttt) REVERT: C 66 HIS cc_start: 0.6814 (OUTLIER) cc_final: 0.6214 (t70) REVERT: C 215 ASP cc_start: 0.1227 (OUTLIER) cc_final: 0.0555 (m-30) REVERT: C 351 TYR cc_start: 0.3194 (OUTLIER) cc_final: 0.2349 (p90) REVERT: C 585 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7871 (mt) REVERT: C 856 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.7862 (p0) REVERT: H 120 VAL cc_start: 0.2237 (OUTLIER) cc_final: 0.1922 (p) REVERT: H 165 SER cc_start: 0.2392 (m) cc_final: 0.2127 (t) REVERT: H 182 SER cc_start: 0.0091 (OUTLIER) cc_final: -0.0269 (t) REVERT: I 23 LYS cc_start: 0.3569 (tptt) cc_final: 0.3159 (mttp) REVERT: I 118 VAL cc_start: -0.1114 (OUTLIER) cc_final: -0.1341 (t) REVERT: I 187 LEU cc_start: 0.1534 (OUTLIER) cc_final: 0.0780 (tp) REVERT: I 215 LYS cc_start: 0.2319 (tppt) cc_final: 0.1893 (tptm) REVERT: M 4 MET cc_start: -0.0192 (mmt) cc_final: -0.1321 (ttm) REVERT: M 39 LEU cc_start: -0.0886 (OUTLIER) cc_final: -0.1331 (pp) REVERT: M 77 PHE cc_start: 0.2222 (OUTLIER) cc_final: 0.1840 (p90) REVERT: J 210 LYS cc_start: 0.1454 (OUTLIER) cc_final: 0.0956 (mtpp) REVERT: N 4 MET cc_start: 0.2134 (mmm) cc_final: 0.1438 (ttp) REVERT: N 111 GLU cc_start: 0.2863 (OUTLIER) cc_final: 0.2036 (tm-30) outliers start: 169 outliers final: 121 residues processed: 358 average time/residue: 0.4387 time to fit residues: 272.6302 Evaluate side-chains 322 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 187 time to evaluate : 4.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 77 PHE Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 38 TYR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 248 optimal weight: 0.5980 chunk 125 optimal weight: 0.0770 chunk 81 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 283 optimal weight: 0.0870 chunk 205 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 327 optimal weight: 20.0000 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1002 GLN B 755 GLN B 856 ASN B 935 GLN B1106 GLN C 207 HIS C1002 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35528 Z= 0.176 Angle : 0.636 11.044 48339 Z= 0.312 Chirality : 0.046 0.643 5724 Planarity : 0.004 0.055 6128 Dihedral : 7.285 59.825 6366 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.20 % Favored : 91.34 % Rotamer: Outliers : 4.24 % Allowed : 23.13 % Favored : 72.63 % 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: -1.13 (0.13), residues: 4283 helix: 1.36 (0.21), residues: 691 sheet: 0.26 (0.14), residues: 1224 loop : -2.08 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 56 HIS 0.002 0.001 HIS A 519 PHE 0.020 0.001 PHE A 643 TYR 0.018 0.001 TYR C1067 ARG 0.002 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 205 time to evaluate : 3.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 882 ILE cc_start: 0.9119 (mt) cc_final: 0.8917 (mt) REVERT: B 569 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.6964 (pt) REVERT: B 740 MET cc_start: 0.8294 (ttt) cc_final: 0.7926 (ttt) REVERT: B 1123 SER cc_start: 0.9264 (t) cc_final: 0.8955 (p) REVERT: C 66 HIS cc_start: 0.6770 (OUTLIER) cc_final: 0.6260 (t70) REVERT: C 215 ASP cc_start: 0.1184 (OUTLIER) cc_final: 0.0599 (m-30) REVERT: C 585 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7819 (mt) REVERT: C 856 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.7814 (p0) REVERT: H 120 VAL cc_start: 0.2327 (OUTLIER) cc_final: 0.2018 (p) REVERT: H 165 SER cc_start: 0.2267 (m) cc_final: 0.1974 (t) REVERT: I 23 LYS cc_start: 0.3607 (tptt) cc_final: 0.3188 (mttp) REVERT: I 81 MET cc_start: 0.2886 (mmm) cc_final: 0.2526 (mmm) REVERT: I 118 VAL cc_start: -0.1132 (OUTLIER) cc_final: -0.1366 (t) REVERT: I 187 LEU cc_start: 0.1529 (OUTLIER) cc_final: 0.0781 (tp) REVERT: I 215 LYS cc_start: 0.2551 (tppt) cc_final: 0.2132 (tptm) REVERT: M 4 MET cc_start: -0.0324 (mmt) cc_final: -0.1408 (ttm) REVERT: M 39 LEU cc_start: -0.0924 (OUTLIER) cc_final: -0.1372 (pp) REVERT: M 77 PHE cc_start: 0.2106 (OUTLIER) cc_final: 0.1698 (p90) REVERT: J 210 LYS cc_start: 0.1454 (OUTLIER) cc_final: 0.0962 (mtpp) REVERT: N 4 MET cc_start: 0.1992 (mmm) cc_final: 0.1403 (ttp) REVERT: N 111 GLU cc_start: 0.2693 (OUTLIER) cc_final: 0.1851 (tm-30) outliers start: 160 outliers final: 126 residues processed: 341 average time/residue: 0.4020 time to fit residues: 240.0613 Evaluate side-chains 329 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 191 time to evaluate : 3.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 77 PHE Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 7.9990 chunk 398 optimal weight: 8.9990 chunk 363 optimal weight: 30.0000 chunk 388 optimal weight: 30.0000 chunk 233 optimal weight: 8.9990 chunk 169 optimal weight: 0.2980 chunk 304 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 350 optimal weight: 0.9980 chunk 366 optimal weight: 0.0040 chunk 386 optimal weight: 5.9990 overall best weight: 1.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1002 GLN B 856 ASN C 207 HIS C1002 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 180 GLN ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 161 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35528 Z= 0.210 Angle : 0.648 11.466 48339 Z= 0.319 Chirality : 0.047 0.621 5724 Planarity : 0.004 0.054 6128 Dihedral : 7.126 57.411 6360 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.45 % Favored : 91.10 % Rotamer: Outliers : 4.21 % Allowed : 23.29 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 4283 helix: 1.37 (0.21), residues: 692 sheet: 0.28 (0.14), residues: 1217 loop : -2.03 (0.12), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.007 0.001 HIS H 209 PHE 0.019 0.001 PHE A 86 TYR 0.027 0.001 TYR N 38 ARG 0.002 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 199 time to evaluate : 3.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.4689 (OUTLIER) cc_final: 0.4463 (m-10) REVERT: B 569 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7203 (mp) REVERT: B 740 MET cc_start: 0.8286 (ttt) cc_final: 0.7938 (ttt) REVERT: B 1123 SER cc_start: 0.9270 (t) cc_final: 0.8963 (p) REVERT: C 66 HIS cc_start: 0.6724 (OUTLIER) cc_final: 0.6158 (t70) REVERT: C 215 ASP cc_start: 0.1594 (OUTLIER) cc_final: 0.1125 (m-30) REVERT: C 351 TYR cc_start: 0.2992 (OUTLIER) cc_final: 0.2060 (p90) REVERT: C 547 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7957 (m) REVERT: C 585 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7846 (mt) REVERT: C 856 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.7846 (p0) REVERT: H 120 VAL cc_start: 0.2440 (OUTLIER) cc_final: 0.2122 (p) REVERT: H 165 SER cc_start: 0.2290 (m) cc_final: 0.2008 (t) REVERT: I 23 LYS cc_start: 0.3613 (tptt) cc_final: 0.3230 (mttp) REVERT: I 81 MET cc_start: 0.2558 (mmm) cc_final: 0.2272 (mmm) REVERT: I 118 VAL cc_start: -0.1145 (OUTLIER) cc_final: -0.1372 (t) REVERT: I 187 LEU cc_start: 0.1713 (OUTLIER) cc_final: 0.0988 (tp) REVERT: I 215 LYS cc_start: 0.2554 (tppt) cc_final: 0.2136 (tptm) REVERT: M 39 LEU cc_start: -0.0887 (OUTLIER) cc_final: -0.1357 (pp) REVERT: M 77 PHE cc_start: 0.2168 (OUTLIER) cc_final: 0.1838 (p90) REVERT: J 210 LYS cc_start: 0.1237 (OUTLIER) cc_final: 0.0807 (mtpp) REVERT: N 4 MET cc_start: 0.1708 (mmm) cc_final: 0.1141 (ttm) REVERT: N 111 GLU cc_start: 0.2422 (OUTLIER) cc_final: 0.1571 (tm-30) outliers start: 159 outliers final: 131 residues processed: 336 average time/residue: 0.4191 time to fit residues: 246.5331 Evaluate side-chains 335 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 189 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 77 PHE Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 4.9990 chunk 410 optimal weight: 0.5980 chunk 250 optimal weight: 9.9990 chunk 194 optimal weight: 0.7980 chunk 285 optimal weight: 6.9990 chunk 430 optimal weight: 3.9990 chunk 396 optimal weight: 2.9990 chunk 342 optimal weight: 0.0870 chunk 35 optimal weight: 8.9990 chunk 264 optimal weight: 0.1980 chunk 210 optimal weight: 5.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1002 GLN B 856 ASN C 207 HIS C1002 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 35528 Z= 0.162 Angle : 0.627 12.475 48339 Z= 0.307 Chirality : 0.046 0.601 5724 Planarity : 0.004 0.058 6128 Dihedral : 6.871 57.135 6358 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.13 % Favored : 91.48 % Rotamer: Outliers : 3.84 % Allowed : 23.64 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 4283 helix: 1.52 (0.21), residues: 691 sheet: 0.40 (0.15), residues: 1219 loop : -1.97 (0.12), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.006 0.001 HIS H 209 PHE 0.016 0.001 PHE A 643 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG A 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 200 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.4657 (OUTLIER) cc_final: 0.4439 (m-10) REVERT: A 1113 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7650 (mt0) REVERT: A 1142 GLN cc_start: 0.7379 (tp40) cc_final: 0.7098 (tp-100) REVERT: B 569 ILE cc_start: 0.7526 (mp) cc_final: 0.7034 (mp) REVERT: B 740 MET cc_start: 0.8270 (ttt) cc_final: 0.7908 (ttt) REVERT: B 1123 SER cc_start: 0.9241 (t) cc_final: 0.8927 (p) REVERT: C 66 HIS cc_start: 0.6720 (OUTLIER) cc_final: 0.6221 (t-170) REVERT: C 215 ASP cc_start: 0.1406 (OUTLIER) cc_final: 0.1032 (m-30) REVERT: C 547 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7970 (m) REVERT: C 585 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7804 (mp) REVERT: C 856 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.7751 (p0) REVERT: I 23 LYS cc_start: 0.3622 (tptt) cc_final: 0.3186 (mttp) REVERT: I 118 VAL cc_start: -0.1136 (OUTLIER) cc_final: -0.1347 (t) REVERT: I 187 LEU cc_start: 0.1680 (OUTLIER) cc_final: 0.0929 (tp) REVERT: I 215 LYS cc_start: 0.2498 (tppt) cc_final: 0.2085 (tptm) REVERT: M 39 LEU cc_start: -0.0910 (OUTLIER) cc_final: -0.1230 (pt) REVERT: M 77 PHE cc_start: 0.2309 (OUTLIER) cc_final: 0.2084 (p90) REVERT: J 210 LYS cc_start: 0.1228 (OUTLIER) cc_final: 0.0801 (mtpp) REVERT: N 4 MET cc_start: 0.1665 (mmm) cc_final: 0.1131 (ttm) REVERT: N 111 GLU cc_start: 0.2421 (OUTLIER) cc_final: 0.1565 (tm-30) outliers start: 145 outliers final: 125 residues processed: 324 average time/residue: 0.3995 time to fit residues: 225.0410 Evaluate side-chains 328 residues out of total 3787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 190 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 77 PHE Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 2.9990 chunk 365 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 316 optimal weight: 40.0000 chunk 50 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 343 optimal weight: 30.0000 chunk 143 optimal weight: 30.0000 chunk 352 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A1002 GLN A1101 HIS B 81 ASN B 856 ASN C 207 HIS C1002 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.216915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.176541 restraints weight = 56274.353| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.64 r_work: 0.3801 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 35528 Z= 0.323 Angle : 0.702 11.818 48339 Z= 0.345 Chirality : 0.049 0.639 5724 Planarity : 0.005 0.059 6128 Dihedral : 7.346 58.808 6358 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.48 % Favored : 90.12 % Rotamer: Outliers : 4.29 % Allowed : 23.45 % Favored : 72.26 % 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: -1.17 (0.13), residues: 4283 helix: 1.19 (0.20), residues: 690 sheet: 0.21 (0.14), residues: 1213 loop : -2.03 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 36 HIS 0.006 0.001 HIS H 209 PHE 0.019 0.002 PHE C 855 TYR 0.019 0.002 TYR C1067 ARG 0.004 0.001 ARG B 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8010.54 seconds wall clock time: 146 minutes 20.26 seconds (8780.26 seconds total)