Starting phenix.real_space_refine on Mon Apr 15 09:33:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fae_31502/04_2024/7fae_31502.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fae_31502/04_2024/7fae_31502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fae_31502/04_2024/7fae_31502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fae_31502/04_2024/7fae_31502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fae_31502/04_2024/7fae_31502.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fae_31502/04_2024/7fae_31502.pdb" } resolution = 3.65 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= 0.002 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 144 5.16 5 C 21774 2.51 5 N 5656 2.21 5 O 6778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 154": "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 GLU 224": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "H ARG 102": "NH1" <-> "NH2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "d GLU 70": "OE1" <-> "OE2" Residue "d TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 108": "NH1" <-> "NH2" Residue "d GLU 143": "OE1" <-> "OE2" Residue "d GLU 161": "OE1" <-> "OE2" Residue "d ARG 211": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e ARG 103": "NH1" <-> "NH2" Residue "g GLU 70": "OE1" <-> "OE2" Residue "g TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 108": "NH1" <-> "NH2" Residue "g GLU 143": "OE1" <-> "OE2" Residue "g GLU 161": "OE1" <-> "OE2" Residue "g ARG 211": "NH1" <-> "NH2" Residue "h ARG 102": "NH1" <-> "NH2" Residue "h ARG 103": "NH1" <-> "NH2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 108": "NH1" <-> "NH2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L ARG 211": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 34352 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 52, 'TRANS': 951} Chain breaks: 8 Chain: "B" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 53, 'TRANS': 952} Chain breaks: 8 Chain: "C" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7866 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 954} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1670 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 11, 'TRANS': 210} Chain: "d" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "e" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1666 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 210} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "g" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "h" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1661 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 Chain: "B" 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: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 16.72, per 1000 atoms: 0.49 Number of scatterers: 34352 At special positions: 0 Unit cell: (218.25, 188.18, 219.22, 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 144 16.00 O 6778 8.00 N 5656 7.00 C 21774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.17 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.98 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 88 " distance=2.04 Simple disulfide: pdb=" SG CYS d 134 " - pdb=" SG CYS d 194 " distance=2.04 Simple disulfide: pdb=" SG CYS e 22 " - pdb=" SG CYS e 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 149 " - pdb=" SG CYS e 205 " distance=2.04 Simple disulfide: pdb=" SG CYS g 23 " - pdb=" SG CYS g 88 " distance=2.04 Simple disulfide: pdb=" SG CYS g 134 " - pdb=" SG CYS g 194 " 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=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C1410 " - " NAG C1411 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 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 X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG 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 B 709 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 343 " " NAG C1407 " - " ASN C 603 " " NAG C1408 " - " ASN C 616 " " NAG C1409 " - " ASN C 657 " " NAG C1410 " - " ASN C1074 " " NAG E 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG Q 1 " - " ASN C 709 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1074 " " NAG a 1 " - " ASN B1098 " " NAG b 1 " - " ASN B1134 " Time building additional restraints: 12.92 Conformation dependent library (CDL) restraints added in 6.0 seconds 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8046 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 75 sheets defined 19.6% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.68 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.886A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.620A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.811A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.588A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.582A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.562A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.604A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.354A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 979 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.430A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.885A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.620A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.812A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.588A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.631A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.771A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.633A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.647A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.626A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.886A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.621A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.812A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.587A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 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: 3.965A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.011A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.372A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.664A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 140 Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'H' and resid 211 through 213 No H-bonds generated for 'chain 'H' and resid 211 through 213' Processing helix chain 'd' and resid 79 through 83 Processing helix chain 'd' and resid 121 through 128 removed outlier: 3.634A pdb=" N GLY d 128 " --> pdb=" O GLN d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 183 through 189 removed outlier: 3.503A pdb=" N GLU d 187 " --> pdb=" O LYS d 183 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS d 188 " --> pdb=" O ALA d 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 87 through 91 removed outlier: 3.664A pdb=" N THR e 91 " --> pdb=" O SER e 88 " (cutoff:3.500A) Processing helix chain 'e' and resid 136 through 140 Processing helix chain 'e' and resid 196 through 198 No H-bonds generated for 'chain 'e' and resid 196 through 198' Processing helix chain 'e' and resid 210 through 213 Processing helix chain 'g' and resid 79 through 83 Processing helix chain 'g' and resid 121 through 128 removed outlier: 3.633A pdb=" N GLY g 128 " --> pdb=" O GLN g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 183 through 189 removed outlier: 3.503A pdb=" N GLU g 187 " --> pdb=" O LYS g 183 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS g 188 " --> pdb=" O ALA g 184 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 91 removed outlier: 3.663A pdb=" N THR h 91 " --> pdb=" O SER h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 136 through 140 Processing helix chain 'h' and resid 196 through 198 No H-bonds generated for 'chain 'h' and resid 196 through 198' Processing helix chain 'h' and resid 210 through 213 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.633A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.502A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.151A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.526A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (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 48 through 55 removed outlier: 4.757A pdb=" N THR A 274 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS A 291 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.248A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.665A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.618A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.973A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.664A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.879A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.230A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.329A 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 removed outlier: 6.914A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.818A 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: 6.591A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.569A 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 removed outlier: 5.810A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.059A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.570A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.679A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 327 through 328 removed outlier: 5.338A 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) removed outlier: 6.948A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.618A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.622A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.255A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.539A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.649A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) 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 84 through 85 removed outlier: 3.780A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.572A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.835A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.626A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.611A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AF2, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.780A pdb=" N SER H 189 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.780A pdb=" N SER H 189 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 159 through 163 removed outlier: 3.558A pdb=" N THR H 160 " --> pdb=" O ASN H 208 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS H 205 " --> pdb=" O LYS H 218 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS H 218 " --> pdb=" O CYS H 205 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'd' and resid 4 through 6 removed outlier: 3.645A pdb=" N VAL d 19 " --> pdb=" O ILE d 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE d 75 " --> pdb=" O VAL d 19 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR d 72 " --> pdb=" O SER d 65 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'd' and resid 10 through 11 Processing sheet with id=AF7, first strand: chain 'd' and resid 53 through 54 removed outlier: 6.331A pdb=" N TRP d 35 " --> pdb=" O LEU d 47 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR d 49 " --> pdb=" O LEU d 33 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU d 33 " --> pdb=" O TYR d 49 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN d 38 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR d 85 " --> pdb=" O GLN d 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'd' and resid 114 through 118 removed outlier: 5.601A pdb=" N TYR d 173 " --> pdb=" O ASN d 138 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'd' and resid 154 through 155 removed outlier: 4.769A pdb=" N TRP d 148 " --> pdb=" O GLN d 155 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'e' and resid 3 through 6 removed outlier: 3.625A pdb=" N GLN e 3 " --> pdb=" O SER e 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER e 25 " --> pdb=" O GLN e 3 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'e' and resid 10 through 12 removed outlier: 6.612A pdb=" N TRP e 36 " --> pdb=" O MET e 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'e' and resid 10 through 12 Processing sheet with id=AG4, first strand: chain 'e' and resid 129 through 133 removed outlier: 3.779A pdb=" N SER e 189 " --> pdb=" O CYS e 149 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR e 185 " --> pdb=" O ASP e 153 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'e' and resid 129 through 133 removed outlier: 3.779A pdb=" N SER e 189 " --> pdb=" O CYS e 149 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR e 185 " --> pdb=" O ASP e 153 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'e' and resid 160 through 163 removed outlier: 3.558A pdb=" N THR e 160 " --> pdb=" O ASN e 208 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS e 205 " --> pdb=" O LYS e 218 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS e 218 " --> pdb=" O CYS e 205 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'g' and resid 4 through 5 removed outlier: 3.645A pdb=" N VAL g 19 " --> pdb=" O ILE g 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE g 75 " --> pdb=" O VAL g 19 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR g 72 " --> pdb=" O SER g 65 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'g' and resid 11 through 13 Processing sheet with id=AG9, first strand: chain 'g' and resid 53 through 54 removed outlier: 6.331A pdb=" N TRP g 35 " --> pdb=" O LEU g 47 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR g 49 " --> pdb=" O LEU g 33 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU g 33 " --> pdb=" O TYR g 49 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN g 38 " --> pdb=" O THR g 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR g 85 " --> pdb=" O GLN g 38 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'g' and resid 114 through 118 Processing sheet with id=AH2, first strand: chain 'g' and resid 154 through 155 removed outlier: 4.770A pdb=" N TRP g 148 " --> pdb=" O GLN g 155 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'h' and resid 3 through 6 removed outlier: 3.625A pdb=" N GLN h 3 " --> pdb=" O SER h 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER h 25 " --> pdb=" O GLN h 3 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.611A pdb=" N TRP h 36 " --> pdb=" O MET h 48 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'h' and resid 10 through 12 Processing sheet with id=AH6, first strand: chain 'h' and resid 129 through 133 removed outlier: 3.779A pdb=" N SER h 189 " --> pdb=" O CYS h 149 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR h 185 " --> pdb=" O ASP h 153 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'h' and resid 129 through 133 removed outlier: 3.779A pdb=" N SER h 189 " --> pdb=" O CYS h 149 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR h 185 " --> pdb=" O ASP h 153 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'h' and resid 160 through 163 removed outlier: 3.868A pdb=" N CYS h 205 " --> pdb=" O LYS h 218 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS h 218 " --> pdb=" O CYS h 205 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.646A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.331A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN L 38 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 114 through 118 Processing sheet with id=AI3, first strand: chain 'L' and resid 154 through 155 removed outlier: 4.769A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 1314 hydrogen bonds defined for protein. 3489 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: 17.30 Time building geometry restraints manager: 14.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6044 1.32 - 1.45: 10852 1.45 - 1.58: 18039 1.58 - 1.72: 0 1.72 - 1.85: 183 Bond restraints: 35118 Sorted by residual: bond pdb=" N THR B 478 " pdb=" CA THR B 478 " ideal model delta sigma weight residual 1.458 1.491 -0.034 7.40e-03 1.83e+04 2.08e+01 bond pdb=" N THR A 478 " pdb=" CA THR A 478 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.99e+01 bond pdb=" C THR A 588 " pdb=" N PRO A 589 " ideal model delta sigma weight residual 1.332 1.388 -0.056 1.34e-02 5.57e+03 1.77e+01 bond pdb=" C HIS C1088 " pdb=" N PHE C1089 " ideal model delta sigma weight residual 1.331 1.265 0.066 1.59e-02 3.96e+03 1.74e+01 bond pdb=" N PHE B 329 " pdb=" CA PHE B 329 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.68e+01 ... (remaining 35113 not shown) Histogram of bond angle deviations from ideal: 97.57 - 105.75: 788 105.75 - 113.93: 20253 113.93 - 122.11: 19963 122.11 - 130.29: 6649 130.29 - 138.47: 116 Bond angle restraints: 47769 Sorted by residual: angle pdb=" CA PRO L 8 " pdb=" N PRO L 8 " pdb=" CD PRO L 8 " ideal model delta sigma weight residual 112.00 98.58 13.42 1.40e+00 5.10e-01 9.19e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 122.26 -11.56 1.22e+00 6.72e-01 8.98e+01 angle pdb=" CA PRO A 899 " pdb=" N PRO A 899 " pdb=" CD PRO A 899 " ideal model delta sigma weight residual 112.00 99.28 12.72 1.40e+00 5.10e-01 8.26e+01 angle pdb=" CA PRO H 158 " pdb=" N PRO H 158 " pdb=" CD PRO H 158 " ideal model delta sigma weight residual 112.00 99.32 12.68 1.40e+00 5.10e-01 8.21e+01 angle pdb=" CA PRO C 899 " pdb=" N PRO C 899 " pdb=" CD PRO C 899 " ideal model delta sigma weight residual 112.00 99.49 12.51 1.40e+00 5.10e-01 7.98e+01 ... (remaining 47764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 19076 17.91 - 35.82: 1923 35.82 - 53.73: 497 53.73 - 71.64: 194 71.64 - 89.55: 56 Dihedral angle restraints: 21746 sinusoidal: 9221 harmonic: 12525 Sorted by residual: dihedral pdb=" CA TYR d 94 " pdb=" C TYR d 94 " pdb=" N PRO d 95 " pdb=" CA PRO d 95 " ideal model delta harmonic sigma weight residual -180.00 -113.01 -66.99 0 5.00e+00 4.00e-02 1.80e+02 dihedral pdb=" CA TYR g 94 " pdb=" C TYR g 94 " pdb=" N PRO g 95 " pdb=" CA PRO g 95 " ideal model delta harmonic sigma weight residual -180.00 -113.02 -66.98 0 5.00e+00 4.00e-02 1.79e+02 dihedral pdb=" CA TYR L 94 " pdb=" C TYR L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual -180.00 -113.05 -66.95 0 5.00e+00 4.00e-02 1.79e+02 ... (remaining 21743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5569 0.328 - 0.655: 9 0.655 - 0.983: 3 0.983 - 1.311: 0 1.311 - 1.639: 1 Chirality restraints: 5582 Sorted by residual: chirality pdb=" C1 NAG C1411 " pdb=" O4 NAG C1410 " pdb=" C2 NAG C1411 " pdb=" O5 NAG C1411 " 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 O 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.71e+01 chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.43e+01 ... (remaining 5579 not shown) Planarity restraints: 6124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.195 2.00e-02 2.50e+03 2.12e-01 5.62e+02 pdb=" CG ASN A 343 " 0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.351 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.242 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " -0.118 5.00e-02 4.00e+02 1.64e-01 4.30e+01 pdb=" N PRO L 8 " 0.283 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 816 " -0.113 5.00e-02 4.00e+02 1.59e-01 4.03e+01 pdb=" N PRO C 817 " 0.274 5.00e-02 4.00e+02 pdb=" CA PRO C 817 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO C 817 " -0.076 5.00e-02 4.00e+02 ... (remaining 6121 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 1 1.81 - 2.58: 411 2.58 - 3.36: 42599 3.36 - 4.13: 80648 4.13 - 4.90: 146395 Nonbonded interactions: 270054 Sorted by model distance: nonbonded pdb=" NH1 ARG A 357 " pdb=" OG1 THR B 167 " model vdw 1.041 2.520 nonbonded pdb=" NH1 ARG A 357 " pdb=" CB THR B 167 " model vdw 1.838 3.550 nonbonded pdb=" O GLN A 804 " pdb=" CD PRO A 817 " model vdw 1.904 3.440 nonbonded pdb=" NH1 ARG A 357 " pdb=" CG2 THR B 167 " model vdw 2.017 3.540 nonbonded pdb=" O PRO H 156 " pdb=" CD PRO H 158 " model vdw 2.040 3.440 ... (remaining 270049 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 385 or (resid 386 and (name N or name CA or nam \ e C or name O or name CB )) or resid 387 through 826 or resid 855 through 1146 o \ r resid 1401 through 1408)) selection = (chain 'B' and (resid 27 through 385 or (resid 386 and (name N or name CA or nam \ e C or name O or name CB )) or resid 387 through 620 or resid 641 through 939 or \ resid 944 through 1146 or resid 1401 through 1408)) selection = (chain 'C' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1408)) } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = (chain 'H' and (resid 1 through 155 or (resid 156 and (name N or name CA or name \ C or name O or name CB )) or (resid 158 and (name N or name CA or name C or nam \ e O or name CB )) or resid 159 through 222)) selection = (chain 'e' and (resid 1 through 156 or resid 158 through 222)) selection = (chain 'h' and (resid 1 through 155 or (resid 156 through 158 and (name N or nam \ e CA or name C or name O or name CB )) or resid 159 through 222)) } ncs_group { reference = chain 'L' selection = chain 'd' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.620 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 92.290 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 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 : 0.010 0.117 35118 Z= 0.673 Angle : 1.037 13.467 47769 Z= 0.619 Chirality : 0.071 1.639 5582 Planarity : 0.008 0.164 6080 Dihedral : 16.577 89.552 13547 Min Nonbonded Distance : 1.041 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.15 % Favored : 90.14 % Rotamer: Outliers : 7.89 % Allowed : 10.58 % Favored : 81.53 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -3.13 (0.11), residues: 4250 helix: -2.21 (0.16), residues: 696 sheet: -1.49 (0.14), residues: 1222 loop : -2.40 (0.11), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 104 HIS 0.009 0.002 HIS A1048 PHE 0.034 0.003 PHE d 71 TYR 0.038 0.003 TYR H 32 ARG 0.009 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 642 time to evaluate : 4.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.0880 (OUTLIER) cc_final: 0.0215 (t70) REVERT: A 976 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8447 (m) REVERT: B 369 TYR cc_start: 0.5943 (t80) cc_final: 0.5497 (t80) REVERT: B 697 MET cc_start: 0.8827 (ptm) cc_final: 0.8490 (ptm) REVERT: C 95 THR cc_start: 0.6111 (OUTLIER) cc_final: 0.5822 (m) REVERT: C 158 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.5465 (tpt-90) REVERT: C 357 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7704 (tpp-160) REVERT: C 567 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7864 (ptp-170) REVERT: C 786 LYS cc_start: 0.7562 (mtmt) cc_final: 0.7324 (mttm) REVERT: H 180 GLN cc_start: -0.1784 (mt0) cc_final: -0.2848 (tp40) REVERT: d 141 PRO cc_start: 0.5015 (Cg_exo) cc_final: 0.4767 (Cg_endo) REVERT: d 204 PRO cc_start: 0.2173 (Cg_exo) cc_final: 0.1920 (Cg_endo) REVERT: e 81 MET cc_start: 0.3621 (tmm) cc_final: 0.2931 (tpp) REVERT: g 54 LEU cc_start: 0.7990 (tp) cc_final: 0.7671 (mm) REVERT: g 83 PHE cc_start: 0.6353 (m-10) cc_final: 0.5975 (m-80) REVERT: g 140 TYR cc_start: 0.4841 (t80) cc_final: 0.4519 (t80) REVERT: h 72 ARG cc_start: 0.7261 (pmt-80) cc_final: 0.7032 (ptt90) REVERT: h 110 ASP cc_start: 0.6833 (p0) cc_final: 0.6307 (p0) outliers start: 296 outliers final: 54 residues processed: 874 average time/residue: 0.4887 time to fit residues: 681.2898 Evaluate side-chains 329 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 269 time to evaluate : 3.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 9.9990 chunk 325 optimal weight: 8.9990 chunk 180 optimal weight: 0.7980 chunk 111 optimal weight: 0.2980 chunk 219 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 336 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 389 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 641 ASN A 690 GLN A 703 ASN A 751 ASN A 901 GLN A 914 ASN A 926 GLN A 992 GLN A1010 GLN A1071 GLN A1101 HIS B 134 GLN B 137 ASN B 188 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 690 GLN B 703 ASN B 856 ASN B 901 GLN B 914 ASN B 919 ASN B 926 GLN B 955 ASN B 969 ASN B 992 GLN B1005 GLN B1106 GLN C 66 HIS C 115 GLN C 188 ASN C 360 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 540 ASN C 563 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 901 GLN C 914 ASN C 919 ASN C 920 GLN C 926 GLN C 992 GLN C1054 GLN H 57 ASN d 3 GLN d 37 GLN ** d 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 39 GLN e 57 ASN ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 6 GLN g 37 GLN ** g 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 1 GLN ** h 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 ASN ** h 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35118 Z= 0.235 Angle : 0.767 13.147 47769 Z= 0.384 Chirality : 0.050 0.469 5582 Planarity : 0.006 0.119 6080 Dihedral : 8.992 65.255 6010 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.36 % Favored : 94.47 % Rotamer: Outliers : 3.68 % Allowed : 16.01 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % 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: -1.90 (0.12), residues: 4250 helix: -0.21 (0.19), residues: 695 sheet: -0.84 (0.14), residues: 1256 loop : -1.87 (0.12), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP d 35 HIS 0.010 0.001 HIS H 35 PHE 0.030 0.002 PHE A 400 TYR 0.023 0.002 TYR C 380 ARG 0.006 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 301 time to evaluate : 3.577 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: A 131 CYS cc_start: 0.0317 (OUTLIER) cc_final: -0.0150 (m) REVERT: A 697 MET cc_start: 0.7976 (ptm) cc_final: 0.7593 (ptm) REVERT: A 902 MET cc_start: 0.8988 (tpp) cc_final: 0.8310 (tpt) REVERT: A 976 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8593 (m) REVERT: A 979 ASP cc_start: 0.7564 (m-30) cc_final: 0.7298 (m-30) REVERT: A 1077 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8389 (m) REVERT: B 697 MET cc_start: 0.8843 (ptm) cc_final: 0.8444 (ptm) REVERT: B 980 ILE cc_start: 0.8302 (mt) cc_final: 0.8071 (mt) REVERT: C 902 MET cc_start: 0.9168 (tpp) cc_final: 0.8958 (tpt) REVERT: H 180 GLN cc_start: -0.1686 (mt0) cc_final: -0.2976 (tp40) REVERT: d 116 PHE cc_start: 0.2744 (m-80) cc_final: 0.2222 (m-80) REVERT: e 36 TRP cc_start: 0.2670 (m100) cc_final: 0.2335 (m100) REVERT: e 44 ARG cc_start: 0.1885 (ptm-80) cc_final: 0.1676 (ptm160) REVERT: e 48 MET cc_start: 0.4068 (mmm) cc_final: 0.3808 (mtp) REVERT: e 50 TRP cc_start: 0.4679 (OUTLIER) cc_final: 0.4096 (p-90) REVERT: e 81 MET cc_start: 0.3128 (tmm) cc_final: 0.2860 (tmm) REVERT: h 72 ARG cc_start: 0.7434 (pmt-80) cc_final: 0.7087 (ptt90) REVERT: h 110 ASP cc_start: 0.7577 (p0) cc_final: 0.6785 (p0) outliers start: 138 outliers final: 69 residues processed: 425 average time/residue: 0.4800 time to fit residues: 334.9959 Evaluate side-chains 296 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 223 time to evaluate : 4.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 94 TYR Chi-restraints excluded: chain g residue 210 ASN Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 324 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 390 optimal weight: 20.0000 chunk 421 optimal weight: 8.9990 chunk 347 optimal weight: 30.0000 chunk 387 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 313 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 969 ASN A1106 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B1106 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 762 GLN C 784 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN ** d 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 208 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 35118 Z= 0.290 Angle : 0.712 15.217 47769 Z= 0.353 Chirality : 0.049 0.477 5582 Planarity : 0.005 0.108 6080 Dihedral : 7.757 60.763 5951 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.05 % Favored : 93.81 % Rotamer: Outliers : 4.13 % Allowed : 17.03 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -1.35 (0.12), residues: 4250 helix: 0.71 (0.20), residues: 690 sheet: -0.51 (0.14), residues: 1313 loop : -1.68 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP h 163 HIS 0.041 0.002 HIS C 66 PHE 0.021 0.002 PHE A 562 TYR 0.022 0.002 TYR B1067 ARG 0.008 0.001 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 251 time to evaluate : 3.930 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: A 902 MET cc_start: 0.8934 (tpp) cc_final: 0.8694 (tpt) REVERT: C 358 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8185 (pt) REVERT: H 180 GLN cc_start: -0.1975 (mt0) cc_final: -0.3104 (tp40) REVERT: d 116 PHE cc_start: 0.2738 (m-80) cc_final: 0.2286 (m-80) REVERT: e 81 MET cc_start: 0.3343 (tmm) cc_final: 0.3119 (tpp) REVERT: g 83 PHE cc_start: 0.6432 (m-10) cc_final: 0.6114 (m-80) REVERT: h 72 ARG cc_start: 0.7590 (pmt-80) cc_final: 0.7239 (ptt90) REVERT: h 110 ASP cc_start: 0.7680 (p0) cc_final: 0.6806 (p0) outliers start: 155 outliers final: 99 residues processed: 386 average time/residue: 0.4633 time to fit residues: 293.8060 Evaluate side-chains 292 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 192 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain d residue 27 GLN Chi-restraints excluded: chain d residue 94 TYR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 210 ASN Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain h residue 170 SER Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 94 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 7.9990 chunk 293 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 391 optimal weight: 6.9990 chunk 414 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 371 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 501 ASN A 564 GLN B 121 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 498 GLN B 675 GLN B 755 GLN B1011 GLN C 271 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS C 690 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 6 GLN g 37 GLN ** g 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 62 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 35118 Z= 0.431 Angle : 0.785 15.725 47769 Z= 0.383 Chirality : 0.050 0.501 5582 Planarity : 0.005 0.099 6080 Dihedral : 7.856 63.958 5943 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.16 % Favored : 93.69 % Rotamer: Outliers : 4.93 % Allowed : 17.77 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -1.35 (0.12), residues: 4250 helix: 0.80 (0.20), residues: 700 sheet: -0.53 (0.14), residues: 1350 loop : -1.73 (0.12), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP g 96 HIS 0.017 0.002 HIS C 66 PHE 0.036 0.002 PHE A 392 TYR 0.024 0.002 TYR g 140 ARG 0.010 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 201 time to evaluate : 3.736 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: A 86 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7484 (t80) REVERT: A 902 MET cc_start: 0.8913 (tpp) cc_final: 0.8504 (tpt) REVERT: B 394 ASN cc_start: 0.5235 (OUTLIER) cc_final: 0.4872 (p0) REVERT: C 135 PHE cc_start: 0.5397 (m-80) cc_final: 0.5139 (m-10) REVERT: H 180 GLN cc_start: -0.1783 (mt0) cc_final: -0.3105 (tp40) REVERT: d 116 PHE cc_start: 0.2687 (m-80) cc_final: 0.2268 (m-80) REVERT: g 18 ARG cc_start: 0.7583 (tmm-80) cc_final: 0.6621 (ttp80) REVERT: g 83 PHE cc_start: 0.6521 (m-10) cc_final: 0.6218 (m-80) REVERT: h 32 TYR cc_start: 0.6094 (OUTLIER) cc_final: 0.2827 (t80) REVERT: h 72 ARG cc_start: 0.7718 (pmt-80) cc_final: 0.7365 (ptt90) REVERT: h 110 ASP cc_start: 0.7883 (p0) cc_final: 0.7121 (p0) outliers start: 185 outliers final: 125 residues processed: 362 average time/residue: 0.4593 time to fit residues: 279.5172 Evaluate side-chains 304 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 176 time to evaluate : 4.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain d residue 27 GLN Chi-restraints excluded: chain d residue 94 TYR Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 210 ASN Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 20.0000 chunk 235 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 308 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 353 optimal weight: 30.0000 chunk 286 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 0.3980 chunk 372 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 762 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 6 GLN ** g 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 62 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35118 Z= 0.266 Angle : 0.672 15.788 47769 Z= 0.324 Chirality : 0.047 0.506 5582 Planarity : 0.005 0.089 6080 Dihedral : 7.340 62.553 5934 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.41 % Favored : 94.45 % Rotamer: Outliers : 4.10 % Allowed : 19.10 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -1.11 (0.13), residues: 4250 helix: 1.19 (0.20), residues: 698 sheet: -0.37 (0.14), residues: 1335 loop : -1.63 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP g 96 HIS 0.008 0.001 HIS H 35 PHE 0.024 0.002 PHE C 168 TYR 0.021 0.001 TYR A1067 ARG 0.008 0.000 ARG g 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 204 time to evaluate : 3.828 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: A 86 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7410 (t80) REVERT: A 902 MET cc_start: 0.8846 (tpp) cc_final: 0.8462 (tpt) REVERT: B 697 MET cc_start: 0.8779 (ptm) cc_final: 0.8558 (ptp) REVERT: C 135 PHE cc_start: 0.5384 (m-80) cc_final: 0.5085 (m-10) REVERT: C 474 GLN cc_start: 0.7740 (mt0) cc_final: 0.7343 (tp40) REVERT: H 81 MET cc_start: 0.1858 (tpp) cc_final: 0.1383 (tpp) REVERT: H 180 GLN cc_start: -0.1777 (mt0) cc_final: -0.3121 (tp40) REVERT: d 70 GLU cc_start: 0.4187 (tp30) cc_final: 0.3958 (tp30) REVERT: d 116 PHE cc_start: 0.2653 (m-80) cc_final: 0.2254 (m-80) REVERT: g 18 ARG cc_start: 0.7565 (tmm-80) cc_final: 0.6664 (ttp80) REVERT: h 32 TYR cc_start: 0.5854 (OUTLIER) cc_final: 0.2931 (t80) REVERT: h 72 ARG cc_start: 0.7699 (pmt-80) cc_final: 0.7292 (ptt90) REVERT: h 110 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7047 (p0) REVERT: L 42 LYS cc_start: 0.4247 (OUTLIER) cc_final: 0.3268 (ptmm) REVERT: L 169 LYS cc_start: 0.6989 (pttm) cc_final: 0.6714 (tptp) REVERT: L 190 LYS cc_start: 0.6676 (tptt) cc_final: 0.6077 (ptmt) outliers start: 154 outliers final: 103 residues processed: 338 average time/residue: 0.4643 time to fit residues: 260.7650 Evaluate side-chains 282 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 175 time to evaluate : 4.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain d residue 94 TYR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 210 ASN Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 110 ASP Chi-restraints excluded: chain h residue 170 SER Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 6.9990 chunk 373 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 243 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 415 optimal weight: 7.9990 chunk 344 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 137 optimal weight: 30.0000 chunk 217 optimal weight: 9.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 955 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 62 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 35118 Z= 0.373 Angle : 0.712 15.847 47769 Z= 0.345 Chirality : 0.048 0.519 5582 Planarity : 0.005 0.092 6080 Dihedral : 7.461 60.083 5933 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.42 % Favored : 93.46 % Rotamer: Outliers : 4.58 % Allowed : 19.53 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -1.14 (0.13), residues: 4250 helix: 1.17 (0.20), residues: 699 sheet: -0.37 (0.14), residues: 1332 loop : -1.67 (0.12), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP h 36 HIS 0.007 0.001 HIS H 35 PHE 0.031 0.002 PHE A 140 TYR 0.027 0.002 TYR L 94 ARG 0.007 0.001 ARG h 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 188 time to evaluate : 4.272 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: A 902 MET cc_start: 0.8851 (tpp) cc_final: 0.8447 (tpt) REVERT: B 380 TYR cc_start: 0.3255 (OUTLIER) cc_final: 0.2150 (m-80) REVERT: C 135 PHE cc_start: 0.5687 (m-80) cc_final: 0.5305 (m-10) REVERT: C 153 MET cc_start: 0.5016 (OUTLIER) cc_final: 0.4647 (ttp) REVERT: C 474 GLN cc_start: 0.7693 (mt0) cc_final: 0.7488 (tp40) REVERT: H 70 ILE cc_start: 0.0105 (OUTLIER) cc_final: -0.0967 (pt) REVERT: H 81 MET cc_start: 0.2253 (tpp) cc_final: 0.1776 (tpp) REVERT: d 70 GLU cc_start: 0.3737 (tp30) cc_final: 0.3536 (tp30) REVERT: d 116 PHE cc_start: 0.2635 (m-80) cc_final: 0.2225 (m-80) REVERT: g 18 ARG cc_start: 0.7645 (tmm-80) cc_final: 0.6956 (ttp80) REVERT: g 106 ILE cc_start: 0.4823 (mt) cc_final: 0.4568 (tp) REVERT: h 32 TYR cc_start: 0.6034 (OUTLIER) cc_final: 0.3105 (t80) REVERT: h 110 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7279 (p0) REVERT: L 169 LYS cc_start: 0.7064 (pttm) cc_final: 0.6816 (tptp) outliers start: 172 outliers final: 130 residues processed: 341 average time/residue: 0.4649 time to fit residues: 267.8604 Evaluate side-chains 312 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 177 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 94 TYR Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 32 TYR Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 210 ASN Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 110 ASP Chi-restraints excluded: chain h residue 170 SER Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 236 optimal weight: 5.9990 chunk 303 optimal weight: 40.0000 chunk 234 optimal weight: 4.9990 chunk 349 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 chunk 413 optimal weight: 10.0000 chunk 258 optimal weight: 0.9990 chunk 252 optimal weight: 4.9990 chunk 190 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 498 GLN B 532 ASN B 762 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35118 Z= 0.214 Angle : 0.642 16.025 47769 Z= 0.308 Chirality : 0.046 0.509 5582 Planarity : 0.004 0.094 6080 Dihedral : 7.097 60.195 5933 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.11 % Favored : 94.80 % Rotamer: Outliers : 3.84 % Allowed : 20.20 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -0.94 (0.13), residues: 4250 helix: 1.43 (0.21), residues: 699 sheet: -0.28 (0.14), residues: 1328 loop : -1.55 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP h 36 HIS 0.005 0.001 HIS H 35 PHE 0.019 0.001 PHE C 168 TYR 0.021 0.001 TYR A1067 ARG 0.006 0.000 ARG h 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 204 time to evaluate : 3.825 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: A 902 MET cc_start: 0.8745 (tpp) cc_final: 0.8413 (tpt) REVERT: B 380 TYR cc_start: 0.3355 (OUTLIER) cc_final: 0.2332 (m-80) REVERT: C 135 PHE cc_start: 0.5615 (m-80) cc_final: 0.5359 (m-10) REVERT: C 153 MET cc_start: 0.5112 (OUTLIER) cc_final: 0.4729 (ttp) REVERT: C 474 GLN cc_start: 0.7751 (mt0) cc_final: 0.7397 (tp40) REVERT: H 70 ILE cc_start: -0.0115 (OUTLIER) cc_final: -0.1221 (pt) REVERT: H 180 GLN cc_start: -0.1876 (mt0) cc_final: -0.3253 (tp40) REVERT: d 116 PHE cc_start: 0.2459 (m-80) cc_final: 0.2180 (m-80) REVERT: g 18 ARG cc_start: 0.7619 (tmm-80) cc_final: 0.6995 (ttp80) REVERT: g 83 PHE cc_start: 0.6498 (m-10) cc_final: 0.6092 (m-80) REVERT: g 106 ILE cc_start: 0.4901 (mt) cc_final: 0.4607 (tp) REVERT: h 32 TYR cc_start: 0.5909 (OUTLIER) cc_final: 0.3214 (t80) REVERT: h 72 ARG cc_start: 0.7786 (pmt-80) cc_final: 0.7380 (ptt90) REVERT: h 110 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.6865 (p0) REVERT: h 179 LEU cc_start: 0.3790 (OUTLIER) cc_final: 0.3336 (tp) REVERT: h 219 LYS cc_start: 0.4441 (tptt) cc_final: 0.3206 (mmmt) REVERT: L 42 LYS cc_start: 0.4245 (OUTLIER) cc_final: 0.3244 (ptmm) outliers start: 144 outliers final: 113 residues processed: 332 average time/residue: 0.5040 time to fit residues: 281.5672 Evaluate side-chains 305 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 185 time to evaluate : 3.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 91 TYR Chi-restraints excluded: chain d residue 94 TYR Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 210 ASN Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain h residue 110 ASP Chi-restraints excluded: chain h residue 170 SER Chi-restraints excluded: chain h residue 179 LEU Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 6.9990 chunk 165 optimal weight: 0.6980 chunk 246 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 chunk 281 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 325 optimal weight: 20.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN d 92 ASN ** d 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 35118 Z= 0.303 Angle : 0.675 16.155 47769 Z= 0.324 Chirality : 0.047 0.523 5582 Planarity : 0.005 0.093 6080 Dihedral : 7.131 59.720 5930 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.16 % Favored : 93.72 % Rotamer: Outliers : 4.24 % Allowed : 20.17 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -0.94 (0.13), residues: 4250 helix: 1.46 (0.20), residues: 699 sheet: -0.31 (0.14), residues: 1342 loop : -1.55 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 50 HIS 0.006 0.001 HIS H 35 PHE 0.015 0.002 PHE C 86 TYR 0.030 0.002 TYR L 94 ARG 0.003 0.000 ARG h 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 190 time to evaluate : 3.810 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: A 902 MET cc_start: 0.8776 (tpp) cc_final: 0.8414 (tpt) REVERT: B 380 TYR cc_start: 0.3353 (OUTLIER) cc_final: 0.2265 (m-80) REVERT: C 135 PHE cc_start: 0.5659 (m-80) cc_final: 0.5401 (m-10) REVERT: C 153 MET cc_start: 0.4962 (OUTLIER) cc_final: 0.4529 (ttp) REVERT: H 180 GLN cc_start: -0.2036 (mt0) cc_final: -0.3372 (tp40) REVERT: d 116 PHE cc_start: 0.2461 (m-80) cc_final: 0.2156 (m-80) REVERT: d 196 VAL cc_start: 0.2941 (OUTLIER) cc_final: 0.2635 (t) REVERT: g 18 ARG cc_start: 0.7709 (tmm-80) cc_final: 0.7132 (ttp80) REVERT: g 106 ILE cc_start: 0.4675 (mt) cc_final: 0.4429 (tp) REVERT: h 32 TYR cc_start: 0.5932 (OUTLIER) cc_final: 0.3092 (t80) REVERT: h 110 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.6772 (p0) REVERT: h 164 ASN cc_start: 0.6939 (m-40) cc_final: 0.5678 (t0) REVERT: h 179 LEU cc_start: 0.3957 (OUTLIER) cc_final: 0.3431 (tp) REVERT: h 219 LYS cc_start: 0.4575 (tptt) cc_final: 0.3243 (mmmt) REVERT: L 42 LYS cc_start: 0.4082 (OUTLIER) cc_final: 0.3063 (ptmm) REVERT: L 91 TYR cc_start: 0.3501 (OUTLIER) cc_final: 0.2233 (p90) outliers start: 159 outliers final: 128 residues processed: 326 average time/residue: 0.4633 time to fit residues: 253.5633 Evaluate side-chains 312 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 176 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 91 TYR Chi-restraints excluded: chain d residue 94 TYR Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 210 ASN Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 110 ASP Chi-restraints excluded: chain h residue 170 SER Chi-restraints excluded: chain h residue 179 LEU Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 30.0000 chunk 396 optimal weight: 9.9990 chunk 361 optimal weight: 10.0000 chunk 385 optimal weight: 7.9990 chunk 231 optimal weight: 7.9990 chunk 167 optimal weight: 0.3980 chunk 302 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 348 optimal weight: 1.9990 chunk 364 optimal weight: 6.9990 chunk 383 optimal weight: 6.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A1088 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 804 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 35118 Z= 0.470 Angle : 0.771 16.713 47769 Z= 0.373 Chirality : 0.050 0.578 5582 Planarity : 0.005 0.092 6080 Dihedral : 7.679 63.074 5930 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.58 % Favored : 92.31 % Rotamer: Outliers : 4.42 % Allowed : 20.06 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -1.21 (0.13), residues: 4250 helix: 1.13 (0.20), residues: 702 sheet: -0.42 (0.14), residues: 1309 loop : -1.72 (0.12), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP e 36 HIS 0.008 0.002 HIS H 35 PHE 0.019 0.002 PHE A 140 TYR 0.025 0.002 TYR A 200 ARG 0.006 0.001 ARG h 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 174 time to evaluate : 3.933 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: A 902 MET cc_start: 0.8900 (tpp) cc_final: 0.8395 (tpt) REVERT: B 380 TYR cc_start: 0.3326 (OUTLIER) cc_final: 0.2170 (m-80) REVERT: C 153 MET cc_start: 0.4780 (OUTLIER) cc_final: 0.4416 (ttp) REVERT: C 440 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8140 (p0) REVERT: d 70 GLU cc_start: 0.4212 (tp30) cc_final: 0.3879 (tp30) REVERT: d 116 PHE cc_start: 0.2488 (m-80) cc_final: 0.2213 (m-80) REVERT: e 131 PHE cc_start: 0.5395 (OUTLIER) cc_final: 0.5004 (m-80) REVERT: g 18 ARG cc_start: 0.7802 (tmm-80) cc_final: 0.7518 (ttp80) REVERT: h 32 TYR cc_start: 0.6088 (OUTLIER) cc_final: 0.4482 (m-80) REVERT: h 110 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6799 (p0) REVERT: h 164 ASN cc_start: 0.7122 (m-40) cc_final: 0.5853 (t0) REVERT: h 179 LEU cc_start: 0.4165 (OUTLIER) cc_final: 0.3662 (tp) REVERT: h 219 LYS cc_start: 0.4872 (tptt) cc_final: 0.3526 (mmmm) REVERT: L 91 TYR cc_start: 0.3927 (OUTLIER) cc_final: 0.2470 (p90) REVERT: L 188 LYS cc_start: 0.3947 (tttt) cc_final: 0.2777 (mttt) outliers start: 166 outliers final: 143 residues processed: 324 average time/residue: 0.4437 time to fit residues: 242.4209 Evaluate side-chains 315 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 164 time to evaluate : 3.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 62 PHE Chi-restraints excluded: chain d residue 91 TYR Chi-restraints excluded: chain d residue 94 TYR Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 131 PHE Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 210 ASN Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 106 PHE Chi-restraints excluded: chain h residue 110 ASP Chi-restraints excluded: chain h residue 170 SER Chi-restraints excluded: chain h residue 179 LEU Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 1.9990 chunk 407 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 chunk 283 optimal weight: 6.9990 chunk 427 optimal weight: 20.0000 chunk 393 optimal weight: 9.9990 chunk 340 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 262 optimal weight: 0.7980 chunk 208 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 409 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 334 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.6769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 35118 Z= 0.362 Angle : 0.709 16.733 47769 Z= 0.342 Chirality : 0.048 0.557 5582 Planarity : 0.005 0.089 6080 Dihedral : 7.502 65.932 5928 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.98 % Favored : 93.91 % Rotamer: Outliers : 4.00 % Allowed : 20.60 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: 4250 helix: 1.23 (0.20), residues: 711 sheet: -0.44 (0.14), residues: 1317 loop : -1.69 (0.12), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP h 36 HIS 0.008 0.001 HIS H 35 PHE 0.025 0.002 PHE C 133 TYR 0.025 0.002 TYR L 94 ARG 0.010 0.001 ARG h 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 177 time to evaluate : 3.826 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: A 902 MET cc_start: 0.8809 (tpp) cc_final: 0.8443 (tpt) REVERT: B 380 TYR cc_start: 0.3486 (OUTLIER) cc_final: 0.2070 (m-80) REVERT: C 153 MET cc_start: 0.4854 (OUTLIER) cc_final: 0.4470 (ttp) REVERT: C 440 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8090 (p0) REVERT: d 70 GLU cc_start: 0.4041 (tp30) cc_final: 0.3728 (tp30) REVERT: d 116 PHE cc_start: 0.2457 (m-80) cc_final: 0.2177 (m-80) REVERT: e 35 HIS cc_start: 0.4500 (OUTLIER) cc_final: 0.4039 (t70) REVERT: g 18 ARG cc_start: 0.7800 (tmm-80) cc_final: 0.7496 (ttp80) REVERT: h 32 TYR cc_start: 0.5895 (OUTLIER) cc_final: 0.4338 (m-80) REVERT: h 72 ARG cc_start: 0.7835 (pmt-80) cc_final: 0.7531 (ppt170) REVERT: h 87 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7447 (mpt180) REVERT: h 110 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.6810 (p0) REVERT: h 164 ASN cc_start: 0.7148 (m-40) cc_final: 0.5857 (t0) REVERT: h 179 LEU cc_start: 0.4099 (OUTLIER) cc_final: 0.3623 (tp) REVERT: h 219 LYS cc_start: 0.4852 (tptt) cc_final: 0.3576 (mmmm) REVERT: L 188 LYS cc_start: 0.3813 (tttt) cc_final: 0.2649 (mttt) outliers start: 150 outliers final: 134 residues processed: 311 average time/residue: 0.4495 time to fit residues: 234.8662 Evaluate side-chains 307 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 166 time to evaluate : 4.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 91 TYR Chi-restraints excluded: chain d residue 94 TYR Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 210 ASN Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 106 PHE Chi-restraints excluded: chain h residue 110 ASP Chi-restraints excluded: chain h residue 170 SER Chi-restraints excluded: chain h residue 179 LEU Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 3.9990 chunk 362 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 313 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 340 optimal weight: 8.9990 chunk 142 optimal weight: 0.0070 chunk 350 optimal weight: 30.0000 chunk 43 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.123348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.095367 restraints weight = 118129.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.090109 restraints weight = 139482.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.085808 restraints weight = 100010.872| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35118 Z= 0.205 Angle : 0.655 16.268 47769 Z= 0.314 Chirality : 0.047 0.515 5582 Planarity : 0.005 0.107 6080 Dihedral : 7.047 65.725 5928 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.46 % Favored : 94.40 % Rotamer: Outliers : 3.70 % Allowed : 21.00 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -0.89 (0.13), residues: 4250 helix: 1.58 (0.21), residues: 706 sheet: -0.32 (0.14), residues: 1334 loop : -1.52 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP h 36 HIS 0.005 0.001 HIS g 189 PHE 0.018 0.001 PHE B 515 TYR 0.025 0.001 TYR L 94 ARG 0.009 0.000 ARG h 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7040.71 seconds wall clock time: 130 minutes 21.60 seconds (7821.60 seconds total)