Starting phenix.real_space_refine on Mon Apr 15 11:38:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czv_30518/04_2024/7czv_30518.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czv_30518/04_2024/7czv_30518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czv_30518/04_2024/7czv_30518.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czv_30518/04_2024/7czv_30518.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czv_30518/04_2024/7czv_30518.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czv_30518/04_2024/7czv_30518.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 21960 2.51 5 N 5685 2.21 5 O 6880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 105": "OE1" <-> "OE2" Residue "K GLU 165": "OE1" <-> "OE2" Residue "K PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 6": "OE1" <-> "OE2" Residue "I ARG 19": "NH1" <-> "NH2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I ARG 87": "NH1" <-> "NH2" Residue "I ARG 98": "NH1" <-> "NH2" Residue "M PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 105": "OE1" <-> "OE2" Residue "M GLU 165": "OE1" <-> "OE2" Residue "M PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 6": "OE1" <-> "OE2" Residue "J ARG 19": "NH1" <-> "NH2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ARG 87": "NH1" <-> "NH2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 105": "OE1" <-> "OE2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "N PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 34672 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7870 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1710 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 13, 'TRANS': 215} Chain: "K" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "I" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1710 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 13, 'TRANS': 215} Chain: "M" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "J" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1710 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 13, 'TRANS': 215} Chain: "N" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 17.61, per 1000 atoms: 0.51 Number of scatterers: 34672 At special positions: 0 Unit cell: (147.832, 171.746, 238.053, 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 147 16.00 O 6880 8.00 N 5685 7.00 C 21960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.17 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=2.11 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.14 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.09 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=2.32 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.08 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.08 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.17 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.10 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.55 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 154 " - pdb=" SG CYS I 210 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.55 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 154 " - pdb=" SG CYS J 210 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.56 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A1406 " - " NAG A1407 " " NAG B1409 " - " NAG B1410 " " NAG C1406 " - " NAG C1407 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-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 331 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 616 " " NAG A1410 " - " ASN A 657 " " NAG A1411 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 331 " " NAG C1408 " - " ASN C 603 " " NAG C1409 " - " ASN C 616 " " NAG C1410 " - " ASN C 657 " " NAG D 1 " - " ASN A 343 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 709 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1098 " " NAG V 1 " - " ASN B1134 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 709 " " NAG Y 1 " - " ASN C 717 " " NAG Z 1 " - " ASN C 801 " " NAG a 1 " - " ASN C1074 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " Time building additional restraints: 14.68 Conformation dependent library (CDL) restraints added in 5.6 seconds 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8108 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 79 sheets defined 17.9% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.45 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.632A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.770A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.636A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.645A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.627A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 993 through 1033 removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.648A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.601A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.011A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.371A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.583A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.718A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.604A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 201 through 203 No H-bonds generated for 'chain 'H' and resid 201 through 203' Processing helix chain 'K' and resid 121 through 128 Processing helix chain 'K' and resid 183 through 187 Processing helix chain 'I' and resid 201 through 203 No H-bonds generated for 'chain 'I' and resid 201 through 203' Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 183 through 187 Processing helix chain 'J' and resid 201 through 203 No H-bonds generated for 'chain 'J' and resid 201 through 203' Processing helix chain 'N' and resid 121 through 128 Processing helix chain 'N' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.570A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.680A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.336A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.255A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.609A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 92 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.516A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN B 280 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE B 285 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 166 through 170 removed outlier: 4.820A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.572A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.654A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.219A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.577A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.557A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.534A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 132 through 135 removed outlier: 4.139A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 193 through 194 removed outlier: 5.992A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 275 through 279 removed outlier: 3.888A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.118A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.605A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.567A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF5, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AF6, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AF7, first strand: chain 'H' and resid 46 through 51 removed outlier: 6.652A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA H 151 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 198 " --> pdb=" O ALA H 151 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 153 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 196 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU H 155 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 194 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 157 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 192 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA H 151 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 198 " --> pdb=" O ALA H 151 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 153 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 196 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU H 155 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 194 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 157 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 192 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 164 through 168 Processing sheet with id=AG2, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AG3, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.680A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN K 38 " --> pdb=" O THR K 85 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 114 through 118 Processing sheet with id=AG5, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AG6, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AG7, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AG8, first strand: chain 'I' and resid 46 through 51 removed outlier: 6.652A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA I 151 " --> pdb=" O VAL I 198 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL I 198 " --> pdb=" O ALA I 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 153 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL I 196 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU I 155 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER I 194 " --> pdb=" O LEU I 155 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS I 157 " --> pdb=" O LEU I 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU I 192 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA I 151 " --> pdb=" O VAL I 198 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL I 198 " --> pdb=" O ALA I 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 153 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL I 196 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU I 155 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER I 194 " --> pdb=" O LEU I 155 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS I 157 " --> pdb=" O LEU I 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU I 192 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 164 through 168 Processing sheet with id=AH3, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AH4, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.680A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN M 38 " --> pdb=" O THR M 85 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'M' and resid 114 through 118 Processing sheet with id=AH6, first strand: chain 'M' and resid 153 through 154 Processing sheet with id=AH7, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AH8, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AH9, first strand: chain 'J' and resid 46 through 51 removed outlier: 6.652A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA J 151 " --> pdb=" O VAL J 198 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL J 198 " --> pdb=" O ALA J 151 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 153 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL J 196 " --> pdb=" O GLY J 153 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU J 155 " --> pdb=" O SER J 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 194 " --> pdb=" O LEU J 155 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS J 157 " --> pdb=" O LEU J 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU J 192 " --> pdb=" O LYS J 157 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA J 151 " --> pdb=" O VAL J 198 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL J 198 " --> pdb=" O ALA J 151 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 153 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL J 196 " --> pdb=" O GLY J 153 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU J 155 " --> pdb=" O SER J 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 194 " --> pdb=" O LEU J 155 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS J 157 " --> pdb=" O LEU J 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU J 192 " --> pdb=" O LYS J 157 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 164 through 168 Processing sheet with id=AI4, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AI5, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.679A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN N 38 " --> pdb=" O THR N 85 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 114 through 118 Processing sheet with id=AI7, first strand: chain 'N' and resid 153 through 154 1220 hydrogen bonds defined for protein. 3210 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: 16.59 Time building geometry restraints manager: 15.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5801 1.32 - 1.45: 10417 1.45 - 1.58: 19019 1.58 - 1.71: 3 1.71 - 1.85: 186 Bond restraints: 35426 Sorted by residual: bond pdb=" CA HIS B 49 " pdb=" C HIS B 49 " ideal model delta sigma weight residual 1.520 1.406 0.115 1.22e-02 6.72e+03 8.88e+01 bond pdb=" CA GLN C 239 " pdb=" C GLN C 239 " ideal model delta sigma weight residual 1.525 1.421 0.104 1.11e-02 8.12e+03 8.85e+01 bond pdb=" CA ASN C 30 " pdb=" C ASN C 30 " ideal model delta sigma weight residual 1.520 1.415 0.105 1.16e-02 7.43e+03 8.15e+01 bond pdb=" CA TYR B 204 " pdb=" C TYR B 204 " ideal model delta sigma weight residual 1.523 1.421 0.102 1.18e-02 7.18e+03 7.46e+01 bond pdb=" CA ARG C 44 " pdb=" C ARG C 44 " ideal model delta sigma weight residual 1.521 1.414 0.107 1.24e-02 6.50e+03 7.42e+01 ... (remaining 35421 not shown) Histogram of bond angle deviations from ideal: 96.93 - 105.30: 838 105.30 - 113.67: 19907 113.67 - 122.04: 20397 122.04 - 130.40: 6918 130.40 - 138.77: 126 Bond angle restraints: 48186 Sorted by residual: angle pdb=" CA PHE C 32 " pdb=" CB PHE C 32 " pdb=" CG PHE C 32 " ideal model delta sigma weight residual 113.80 103.52 10.28 1.00e+00 1.00e+00 1.06e+02 angle pdb=" CA GLN C 271 " pdb=" C GLN C 271 " pdb=" N PRO C 272 " ideal model delta sigma weight residual 117.82 125.24 -7.42 7.80e-01 1.64e+00 9.04e+01 angle pdb=" CA GLU C 224 " pdb=" C GLU C 224 " pdb=" O GLU C 224 " ideal model delta sigma weight residual 120.19 112.60 7.59 8.40e-01 1.42e+00 8.17e+01 angle pdb=" CA ASN B 188 " pdb=" CB ASN B 188 " pdb=" CG ASN B 188 " ideal model delta sigma weight residual 112.60 103.64 8.96 1.00e+00 1.00e+00 8.02e+01 angle pdb=" CA PHE C 238 " pdb=" CB PHE C 238 " pdb=" CG PHE C 238 " ideal model delta sigma weight residual 113.80 122.38 -8.58 1.00e+00 1.00e+00 7.37e+01 ... (remaining 48181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 19066 17.91 - 35.83: 2131 35.83 - 53.74: 615 53.74 - 71.66: 207 71.66 - 89.57: 62 Dihedral angle restraints: 22081 sinusoidal: 9462 harmonic: 12619 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.11 71.89 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual 93.00 35.69 57.31 1 1.00e+01 1.00e-02 4.42e+01 dihedral pdb=" N ASP B 198 " pdb=" C ASP B 198 " pdb=" CA ASP B 198 " pdb=" CB ASP B 198 " ideal model delta harmonic sigma weight residual 122.80 138.64 -15.84 0 2.50e+00 1.60e-01 4.02e+01 ... (remaining 22078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5629 0.328 - 0.656: 30 0.656 - 0.984: 5 0.984 - 1.312: 3 1.312 - 1.640: 3 Chirality restraints: 5670 Sorted by residual: chirality pdb=" C1 NAG C1407 " pdb=" O4 NAG C1406 " pdb=" C2 NAG C1407 " pdb=" O5 NAG C1407 " both_signs ideal model delta sigma weight residual False -2.40 -3.44 1.04 2.00e-02 2.50e+03 2.72e+03 chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-02 2.50e+03 9.65e+02 ... (remaining 5667 not shown) Planarity restraints: 6185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " -0.190 2.00e-02 2.50e+03 2.35e-01 6.93e+02 pdb=" CG ASN C 657 " 0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " 0.388 2.00e-02 2.50e+03 pdb=" C1 NAG C1410 " -0.291 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " -0.041 2.00e-02 2.50e+03 2.27e-01 6.47e+02 pdb=" CG ASN B 122 " 0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " -0.167 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " 0.401 2.00e-02 2.50e+03 pdb=" C1 NAG B1402 " -0.254 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 122 " 0.074 2.00e-02 2.50e+03 2.03e-01 5.14e+02 pdb=" CG ASN C 122 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN C 122 " 0.113 2.00e-02 2.50e+03 pdb=" ND2 ASN C 122 " -0.361 2.00e-02 2.50e+03 pdb=" C1 NAG C1402 " 0.232 2.00e-02 2.50e+03 ... (remaining 6182 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 392 2.51 - 3.11: 25755 3.11 - 3.71: 50214 3.71 - 4.30: 74604 4.30 - 4.90: 124209 Nonbonded interactions: 275174 Sorted by model distance: nonbonded pdb=" O ARG C 273 " pdb=" OG1 THR C 274 " model vdw 1.913 2.440 nonbonded pdb=" O ASP I 62 " pdb=" OG SER I 63 " model vdw 1.945 2.440 nonbonded pdb=" O ASP H 62 " pdb=" OG SER H 63 " model vdw 1.945 2.440 nonbonded pdb=" O ASP J 62 " pdb=" OG SER J 63 " model vdw 1.945 2.440 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.982 2.520 ... (remaining 275169 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 620 or resid 641 through 939 or resid 944 throu \ gh 1146 or resid 1401 through 1410)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1410)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1146 or resid 1401 thr \ ough 1410)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 7.290 Check model and map are aligned: 0.520 Set scattering table: 0.290 Process input model: 93.460 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.500 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: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.118 35426 Z= 0.788 Angle : 1.264 13.771 48186 Z= 0.762 Chirality : 0.089 1.640 5670 Planarity : 0.009 0.185 6137 Dihedral : 17.446 89.571 13820 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 31.73 Ramachandran Plot: Outliers : 2.94 % Allowed : 11.36 % Favored : 85.70 % Rotamer: Outliers : 11.76 % Allowed : 16.17 % Favored : 72.07 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.11), residues: 4280 helix: -2.26 (0.16), residues: 683 sheet: -1.88 (0.13), residues: 1364 loop : -3.22 (0.11), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.166 0.005 TRP C 64 HIS 0.008 0.002 HIS A1048 PHE 0.119 0.005 PHE C 220 TYR 0.091 0.003 TYR C 38 ARG 0.011 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 445 poor density : 678 time to evaluate : 3.754 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: A 153 MET cc_start: 0.0165 (mpp) cc_final: -0.0870 (ttp) REVERT: A 517 LEU cc_start: 0.4391 (OUTLIER) cc_final: 0.3844 (pt) REVERT: A 572 THR cc_start: 0.7423 (p) cc_final: 0.6955 (p) REVERT: A 886 TRP cc_start: 0.5457 (p90) cc_final: 0.5074 (p90) REVERT: A 902 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5748 (tpt) REVERT: B 197 ILE cc_start: 0.6595 (mm) cc_final: 0.6308 (tt) REVERT: B 529 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.4921 (mmtt) REVERT: B 547 THR cc_start: 0.6455 (m) cc_final: 0.6209 (p) REVERT: B 606 ASN cc_start: 0.7001 (OUTLIER) cc_final: 0.6526 (t0) REVERT: B 676 THR cc_start: 0.6071 (OUTLIER) cc_final: 0.5803 (m) REVERT: B 1094 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7288 (m) REVERT: C 770 ILE cc_start: 0.6815 (OUTLIER) cc_final: 0.6438 (pt) REVERT: C 856 ASN cc_start: 0.6752 (OUTLIER) cc_final: 0.6383 (p0) REVERT: C 973 ILE cc_start: 0.7510 (pt) cc_final: 0.7304 (pt) REVERT: H 193 SER cc_start: 0.0623 (OUTLIER) cc_final: 0.0359 (p) REVERT: I 83 MET cc_start: -0.0083 (mtm) cc_final: -0.1018 (tmm) REVERT: I 105 MET cc_start: 0.0957 (mtp) cc_final: 0.0538 (mpp) REVERT: I 209 ILE cc_start: 0.3104 (OUTLIER) cc_final: 0.2605 (tp) REVERT: M 6 GLN cc_start: 0.4252 (mt0) cc_final: 0.3448 (tp40) REVERT: J 107 GLN cc_start: 0.6002 (OUTLIER) cc_final: 0.5763 (mm110) REVERT: J 217 SER cc_start: 0.0036 (OUTLIER) cc_final: -0.0342 (t) REVERT: N 27 GLN cc_start: 0.0774 (pm20) cc_final: 0.0485 (pt0) REVERT: N 50 ASP cc_start: 0.5056 (OUTLIER) cc_final: 0.4252 (p0) REVERT: N 65 SER cc_start: 0.4971 (t) cc_final: 0.4623 (m) REVERT: N 103 LYS cc_start: 0.4625 (tptp) cc_final: 0.4190 (mttt) outliers start: 445 outliers final: 86 residues processed: 1032 average time/residue: 0.4424 time to fit residues: 753.0308 Evaluate side-chains 436 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 337 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 217 PRO Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 159 SER Chi-restraints excluded: chain J residue 107 GLN Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain J residue 217 SER Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 142 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 10.0000 chunk 325 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 336 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 250 optimal weight: 3.9990 chunk 389 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 164 ASN A 188 ASN A 394 ASN A 422 ASN A 498 GLN A 607 GLN A 644 GLN A 658 ASN A 690 GLN A 703 ASN A 762 GLN A 787 GLN A 856 ASN A 914 ASN A 919 ASN A 926 GLN A 992 GLN B 81 ASN B 115 GLN B 125 ASN B 164 ASN B 188 ASN B 207 HIS B 239 GLN B 245 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 440 ASN B 498 GLN B 675 GLN B 690 GLN B 751 ASN B 755 GLN B 914 ASN B 920 GLN B 926 GLN B 955 ASN B 992 GLN B1054 GLN C 30 ASN C 239 GLN C 245 HIS C 314 GLN C 321 GLN C 354 ASN C 422 ASN C 450 ASN C 498 GLN C 532 ASN C 641 ASN C 655 HIS C 804 GLN C 901 GLN C 907 ASN C 914 ASN C 926 GLN C 935 GLN C 969 ASN C 978 ASN C 992 GLN C1010 GLN C1071 GLN C1088 HIS H 57 ASN H 101 GLN I 57 ASN I 82 GLN M 90 GLN J 57 ASN J 82 GLN J 107 GLN ** N 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 35426 Z= 0.357 Angle : 0.896 16.533 48186 Z= 0.444 Chirality : 0.055 0.479 5670 Planarity : 0.007 0.067 6137 Dihedral : 9.318 96.609 6306 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.60 % Favored : 90.93 % Rotamer: Outliers : 6.13 % Allowed : 18.92 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.12), residues: 4280 helix: -0.49 (0.19), residues: 693 sheet: -1.07 (0.13), residues: 1334 loop : -2.63 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 35 HIS 0.011 0.002 HIS I 35 PHE 0.023 0.003 PHE A 157 TYR 0.027 0.003 TYR N 49 ARG 0.012 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 334 time to evaluate : 3.889 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 153 MET cc_start: 0.0354 (mpp) cc_final: -0.1087 (ttt) REVERT: A 164 ASN cc_start: 0.4569 (OUTLIER) cc_final: 0.4338 (m-40) REVERT: A 538 CYS cc_start: 0.5744 (t) cc_final: 0.5487 (t) REVERT: A 584 ILE cc_start: 0.7803 (mm) cc_final: 0.7569 (mm) REVERT: A 935 GLN cc_start: 0.7613 (tt0) cc_final: 0.7085 (tt0) REVERT: A 1136 THR cc_start: 0.8433 (p) cc_final: 0.8229 (p) REVERT: B 100 ILE cc_start: 0.6328 (mm) cc_final: 0.5983 (mm) REVERT: B 160 TYR cc_start: 0.3421 (p90) cc_final: 0.2399 (p90) REVERT: B 270 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8078 (mt) REVERT: B 529 LYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5688 (mmtm) REVERT: B 599 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8479 (t) REVERT: C 241 LEU cc_start: 0.6691 (mp) cc_final: 0.6397 (mt) REVERT: C 242 LEU cc_start: 0.5698 (mp) cc_final: 0.5341 (mt) REVERT: C 703 ASN cc_start: 0.7767 (t0) cc_final: 0.7522 (t0) REVERT: C 814 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6954 (mtpt) REVERT: C 1092 GLU cc_start: 0.6329 (tm-30) cc_final: 0.6093 (pp20) REVERT: H 76 LYS cc_start: 0.5701 (tttm) cc_final: 0.5039 (pttt) REVERT: H 207 THR cc_start: 0.1098 (OUTLIER) cc_final: 0.0884 (p) REVERT: K 92 ASP cc_start: 0.2719 (OUTLIER) cc_final: 0.2436 (m-30) REVERT: K 181 LEU cc_start: 0.0453 (OUTLIER) cc_final: -0.0577 (pt) REVERT: I 34 MET cc_start: 0.2426 (mmm) cc_final: 0.1990 (tpp) REVERT: I 83 MET cc_start: -0.0250 (mtm) cc_final: -0.0965 (ttp) REVERT: I 91 THR cc_start: 0.3366 (OUTLIER) cc_final: 0.3124 (t) REVERT: I 105 MET cc_start: 0.0490 (mtp) cc_final: 0.0026 (mpp) REVERT: I 124 THR cc_start: 0.2643 (OUTLIER) cc_final: 0.2375 (t) REVERT: I 184 LEU cc_start: 0.2898 (OUTLIER) cc_final: 0.2516 (pt) REVERT: M 6 GLN cc_start: 0.4361 (mt0) cc_final: 0.3383 (tp40) REVERT: M 32 TYR cc_start: 0.3406 (OUTLIER) cc_final: 0.3188 (p90) REVERT: J 114 PHE cc_start: 0.0853 (m-80) cc_final: 0.0331 (m-80) REVERT: N 27 GLN cc_start: 0.0794 (pm20) cc_final: 0.0432 (pt0) REVERT: N 50 ASP cc_start: 0.5060 (OUTLIER) cc_final: 0.3636 (m-30) REVERT: N 90 GLN cc_start: 0.3083 (pp30) cc_final: 0.2475 (mp10) REVERT: N 103 LYS cc_start: 0.4636 (tptp) cc_final: 0.4183 (mttt) outliers start: 232 outliers final: 110 residues processed: 544 average time/residue: 0.4316 time to fit residues: 397.3858 Evaluate side-chains 358 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 235 time to evaluate : 3.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 116 PHE Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 116 PHE Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 116 PHE Chi-restraints excluded: chain N residue 202 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 324 optimal weight: 10.0000 chunk 265 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 390 optimal weight: 30.0000 chunk 421 optimal weight: 40.0000 chunk 347 optimal weight: 8.9990 chunk 387 optimal weight: 0.0070 chunk 133 optimal weight: 10.0000 chunk 313 optimal weight: 20.0000 overall best weight: 4.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 30 ASN B 280 ASN B 501 ASN B 907 ASN B 955 ASN C 125 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 542 ASN C 606 ASN C 907 ASN C 935 GLN C1002 GLN C1106 GLN H 107 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN K 160 GLN I 107 GLN M 31 ASN ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN M 137 ASN J 39 GLN N 6 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.6168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 35426 Z= 0.438 Angle : 0.838 13.559 48186 Z= 0.418 Chirality : 0.054 0.494 5670 Planarity : 0.006 0.097 6137 Dihedral : 8.244 59.884 6189 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.97 % Favored : 90.70 % Rotamer: Outliers : 6.71 % Allowed : 19.64 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.12), residues: 4280 helix: -0.10 (0.19), residues: 701 sheet: -0.92 (0.14), residues: 1379 loop : -2.39 (0.12), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 353 HIS 0.008 0.002 HIS I 35 PHE 0.032 0.003 PHE B 157 TYR 0.038 0.002 TYR I 53 ARG 0.007 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 263 time to evaluate : 3.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0337 (OUTLIER) cc_final: -0.1615 (ttt) REVERT: A 568 ASP cc_start: 0.7033 (p0) cc_final: 0.6816 (p0) REVERT: A 726 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9022 (mp) REVERT: A 748 GLU cc_start: 0.7278 (mp0) cc_final: 0.7035 (mp0) REVERT: B 533 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7155 (tp) REVERT: B 697 MET cc_start: 0.7888 (ptm) cc_final: 0.7680 (ptp) REVERT: B 722 VAL cc_start: 0.9438 (OUTLIER) cc_final: 0.9063 (t) REVERT: C 242 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.6009 (mp) REVERT: C 518 LEU cc_start: 0.3509 (OUTLIER) cc_final: 0.3108 (mt) REVERT: C 1036 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8863 (tt0) REVERT: C 1132 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8761 (mt) REVERT: H 76 LYS cc_start: 0.5762 (tttm) cc_final: 0.4921 (mtmt) REVERT: H 173 LEU cc_start: 0.0793 (tp) cc_final: 0.0251 (mt) REVERT: H 207 THR cc_start: 0.1035 (OUTLIER) cc_final: 0.0571 (p) REVERT: I 83 MET cc_start: -0.0222 (mtm) cc_final: -0.1079 (ttp) REVERT: I 91 THR cc_start: 0.3553 (OUTLIER) cc_final: 0.3319 (t) REVERT: I 105 MET cc_start: 0.0537 (mtp) cc_final: 0.0197 (mpp) REVERT: I 124 THR cc_start: 0.2450 (OUTLIER) cc_final: 0.2161 (t) REVERT: M 6 GLN cc_start: 0.3878 (mt0) cc_final: 0.3123 (tp40) REVERT: M 100 GLN cc_start: 0.3132 (OUTLIER) cc_final: 0.0023 (tp-100) REVERT: J 130 THR cc_start: 0.2708 (OUTLIER) cc_final: 0.2408 (m) REVERT: N 27 GLN cc_start: 0.0798 (pm20) cc_final: 0.0423 (pt0) REVERT: N 90 GLN cc_start: 0.2839 (pp30) cc_final: 0.2249 (mp10) outliers start: 254 outliers final: 143 residues processed: 489 average time/residue: 0.4247 time to fit residues: 356.0995 Evaluate side-chains 354 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 198 time to evaluate : 3.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1036 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 96 TYR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 159 SER 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: 1.9990 chunk 202 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 chunk 391 optimal weight: 20.0000 chunk 414 optimal weight: 20.0000 chunk 204 optimal weight: 4.9990 chunk 371 optimal weight: 50.0000 chunk 111 optimal weight: 20.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1113 GLN B 613 GLN B1002 GLN B1071 GLN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 607 GLN C1005 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN M 160 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35426 Z= 0.309 Angle : 0.724 12.958 48186 Z= 0.357 Chirality : 0.049 0.467 5670 Planarity : 0.005 0.062 6137 Dihedral : 7.748 59.998 6169 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.71 % Favored : 92.01 % Rotamer: Outliers : 5.58 % Allowed : 20.98 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.12), residues: 4280 helix: 0.33 (0.20), residues: 707 sheet: -0.72 (0.14), residues: 1360 loop : -2.26 (0.12), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 117 HIS 0.006 0.001 HIS I 35 PHE 0.026 0.002 PHE A 643 TYR 0.024 0.002 TYR I 53 ARG 0.005 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 220 time to evaluate : 3.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.5947 (OUTLIER) cc_final: 0.5579 (m-30) REVERT: A 153 MET cc_start: 0.0378 (OUTLIER) cc_final: -0.1580 (ttt) REVERT: A 568 ASP cc_start: 0.7034 (p0) cc_final: 0.6761 (p0) REVERT: A 584 ILE cc_start: 0.7973 (mm) cc_final: 0.7666 (mm) REVERT: A 1144 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6401 (tp30) REVERT: B 342 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.5764 (m-80) REVERT: B 533 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7135 (tp) REVERT: B 599 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8651 (t) REVERT: B 722 VAL cc_start: 0.9384 (OUTLIER) cc_final: 0.9155 (t) REVERT: C 52 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7112 (tm-30) REVERT: C 1036 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8774 (tt0) REVERT: C 1086 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7973 (mtmm) REVERT: C 1132 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8776 (mt) REVERT: H 76 LYS cc_start: 0.5844 (tttm) cc_final: 0.5026 (mtmt) REVERT: H 173 LEU cc_start: 0.1108 (tp) cc_final: 0.0462 (mt) REVERT: H 184 LEU cc_start: 0.2144 (OUTLIER) cc_final: 0.1800 (pt) REVERT: H 207 THR cc_start: 0.1262 (OUTLIER) cc_final: 0.0771 (p) REVERT: I 83 MET cc_start: -0.0438 (mtm) cc_final: -0.1589 (tmm) REVERT: I 91 THR cc_start: 0.4385 (OUTLIER) cc_final: 0.4158 (t) REVERT: I 105 MET cc_start: 0.0507 (mtp) cc_final: 0.0296 (mpp) REVERT: I 124 THR cc_start: 0.2340 (OUTLIER) cc_final: 0.2038 (t) REVERT: M 6 GLN cc_start: 0.4216 (mt0) cc_final: 0.3412 (tp40) REVERT: J 130 THR cc_start: 0.3067 (OUTLIER) cc_final: 0.2759 (m) REVERT: J 211 ASN cc_start: 0.2636 (OUTLIER) cc_final: 0.2325 (t0) REVERT: J 215 LYS cc_start: 0.2206 (OUTLIER) cc_final: 0.1221 (mmtp) REVERT: N 27 GLN cc_start: 0.0840 (pm20) cc_final: 0.0443 (pt0) REVERT: N 90 GLN cc_start: 0.2908 (pp30) cc_final: 0.2210 (mp10) outliers start: 211 outliers final: 131 residues processed: 408 average time/residue: 0.4445 time to fit residues: 307.4898 Evaluate side-chains 346 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 198 time to evaluate : 3.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1036 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 96 TYR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 30.0000 chunk 235 optimal weight: 7.9990 chunk 6 optimal weight: 0.1980 chunk 308 optimal weight: 20.0000 chunk 171 optimal weight: 2.9990 chunk 353 optimal weight: 40.0000 chunk 286 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 3.9990 chunk 372 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 115 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 280 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C1005 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 189 HIS J 39 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.7061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 35426 Z= 0.330 Angle : 0.719 14.216 48186 Z= 0.355 Chirality : 0.049 0.500 5670 Planarity : 0.005 0.059 6137 Dihedral : 7.552 59.590 6163 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.60 % Favored : 91.14 % Rotamer: Outliers : 5.97 % Allowed : 20.77 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.12), residues: 4280 helix: 0.61 (0.20), residues: 699 sheet: -0.63 (0.14), residues: 1351 loop : -2.17 (0.12), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 117 HIS 0.006 0.001 HIS B1048 PHE 0.024 0.002 PHE A 643 TYR 0.020 0.002 TYR B1067 ARG 0.004 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 209 time to evaluate : 3.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6658 (m-70) REVERT: A 153 MET cc_start: 0.0522 (OUTLIER) cc_final: -0.1648 (ttt) REVERT: A 161 SER cc_start: 0.6641 (OUTLIER) cc_final: 0.5967 (p) REVERT: A 584 ILE cc_start: 0.8103 (mm) cc_final: 0.7885 (mm) REVERT: A 726 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9010 (mp) REVERT: A 1144 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6457 (tp30) REVERT: B 342 PHE cc_start: 0.6909 (OUTLIER) cc_final: 0.5771 (m-80) REVERT: B 533 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7234 (tp) REVERT: B 599 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8666 (t) REVERT: B 761 THR cc_start: 0.7879 (m) cc_final: 0.7674 (m) REVERT: B 780 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: C 52 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7038 (tm-30) REVERT: C 332 ILE cc_start: 0.4951 (OUTLIER) cc_final: 0.4704 (mt) REVERT: C 907 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8478 (m-40) REVERT: C 1036 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8790 (tt0) REVERT: C 1086 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7996 (mtmm) REVERT: C 1132 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8814 (mt) REVERT: H 76 LYS cc_start: 0.5928 (tttm) cc_final: 0.5092 (mtmt) REVERT: H 173 LEU cc_start: 0.1121 (tp) cc_final: 0.0491 (mt) REVERT: H 184 LEU cc_start: 0.2644 (OUTLIER) cc_final: 0.2395 (pt) REVERT: H 207 THR cc_start: 0.1197 (OUTLIER) cc_final: 0.0736 (p) REVERT: I 69 THR cc_start: 0.4205 (m) cc_final: 0.3846 (p) REVERT: I 83 MET cc_start: -0.0426 (mtm) cc_final: -0.1496 (tmm) REVERT: I 91 THR cc_start: 0.4454 (OUTLIER) cc_final: 0.4201 (t) REVERT: I 105 MET cc_start: 0.0235 (mtp) cc_final: -0.0041 (mpp) REVERT: M 6 GLN cc_start: 0.4485 (mt0) cc_final: 0.3591 (tp40) REVERT: J 130 THR cc_start: 0.3391 (OUTLIER) cc_final: 0.3053 (m) REVERT: J 215 LYS cc_start: 0.2335 (OUTLIER) cc_final: 0.1287 (mmtp) REVERT: N 27 GLN cc_start: 0.1172 (pm20) cc_final: 0.0806 (pt0) REVERT: N 90 GLN cc_start: 0.2817 (pp30) cc_final: 0.2091 (mp10) REVERT: N 103 LYS cc_start: 0.4586 (tptp) cc_final: 0.4059 (mttt) outliers start: 226 outliers final: 158 residues processed: 415 average time/residue: 0.4215 time to fit residues: 304.1183 Evaluate side-chains 370 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 193 time to evaluate : 4.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1036 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1086 LYS 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 1117 THR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 96 TYR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain N residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 9.9990 chunk 373 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 415 optimal weight: 40.0000 chunk 344 optimal weight: 30.0000 chunk 192 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 493 GLN C 87 ASN C 370 ASN C1005 GLN K 90 GLN K 189 HIS ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.7577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 35426 Z= 0.366 Angle : 0.739 13.619 48186 Z= 0.366 Chirality : 0.050 0.568 5670 Planarity : 0.005 0.059 6137 Dihedral : 7.736 59.912 6160 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.48 % Favored : 91.24 % Rotamer: Outliers : 5.87 % Allowed : 21.19 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.12), residues: 4280 helix: 0.61 (0.20), residues: 698 sheet: -0.54 (0.14), residues: 1329 loop : -2.18 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 117 HIS 0.006 0.001 HIS B1048 PHE 0.027 0.002 PHE A 643 TYR 0.019 0.002 TYR B1067 ARG 0.005 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 213 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7183 (OUTLIER) cc_final: 0.6735 (m-70) REVERT: A 111 ASP cc_start: 0.5992 (OUTLIER) cc_final: 0.5428 (m-30) REVERT: A 153 MET cc_start: 0.0656 (OUTLIER) cc_final: -0.1726 (ttt) REVERT: A 161 SER cc_start: 0.6848 (OUTLIER) cc_final: 0.6215 (p) REVERT: A 364 ASP cc_start: 0.5800 (OUTLIER) cc_final: 0.5319 (t0) REVERT: A 584 ILE cc_start: 0.8278 (mm) cc_final: 0.7976 (mm) REVERT: A 726 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.8995 (mp) REVERT: A 1144 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6693 (tp30) REVERT: B 533 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7449 (tp) REVERT: B 599 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8678 (t) REVERT: B 780 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: C 907 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8482 (m-40) REVERT: C 1036 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8811 (tt0) REVERT: C 1086 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8024 (mtmm) REVERT: C 1132 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8821 (mt) REVERT: H 76 LYS cc_start: 0.5899 (tttm) cc_final: 0.5150 (mtmt) REVERT: H 173 LEU cc_start: 0.1313 (tp) cc_final: 0.0771 (mm) REVERT: K 181 LEU cc_start: 0.0376 (OUTLIER) cc_final: -0.0703 (pt) REVERT: I 69 THR cc_start: 0.4222 (m) cc_final: 0.3848 (p) REVERT: I 80 TYR cc_start: 0.3602 (m-80) cc_final: 0.2877 (m-80) REVERT: M 6 GLN cc_start: 0.4069 (mt0) cc_final: 0.3163 (tp40) REVERT: J 130 THR cc_start: 0.3229 (OUTLIER) cc_final: 0.2857 (m) REVERT: J 215 LYS cc_start: 0.2687 (OUTLIER) cc_final: 0.1453 (mmtp) REVERT: J 228 LYS cc_start: 0.0481 (mttp) cc_final: -0.1688 (tppt) REVERT: N 27 GLN cc_start: 0.1025 (pm20) cc_final: 0.0640 (pt0) REVERT: N 90 GLN cc_start: 0.2841 (pp30) cc_final: 0.2059 (mp10) REVERT: N 103 LYS cc_start: 0.4924 (tptp) cc_final: 0.4457 (mttt) outliers start: 222 outliers final: 167 residues processed: 417 average time/residue: 0.4202 time to fit residues: 300.9656 Evaluate side-chains 385 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 201 time to evaluate : 3.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1036 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1086 LYS 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 1117 THR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 96 TYR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 50.0000 chunk 46 optimal weight: 0.5980 chunk 236 optimal weight: 7.9990 chunk 303 optimal weight: 10.0000 chunk 234 optimal weight: 0.4980 chunk 349 optimal weight: 0.0270 chunk 231 optimal weight: 6.9990 chunk 413 optimal weight: 0.0470 chunk 258 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 422 ASN B 493 GLN B 901 GLN C 644 GLN C 779 GLN C1005 GLN K 24 GLN I 185 GLN M 90 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.7645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35426 Z= 0.153 Angle : 0.632 15.978 48186 Z= 0.310 Chirality : 0.046 0.459 5670 Planarity : 0.004 0.052 6137 Dihedral : 6.867 57.627 6159 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.89 % Favored : 92.90 % Rotamer: Outliers : 3.04 % Allowed : 24.02 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 4280 helix: 1.18 (0.21), residues: 686 sheet: -0.38 (0.14), residues: 1333 loop : -1.93 (0.12), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 168 HIS 0.006 0.001 HIS I 35 PHE 0.017 0.001 PHE A 643 TYR 0.021 0.001 TYR J 116 ARG 0.004 0.000 ARG J 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 226 time to evaluate : 3.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7085 (OUTLIER) cc_final: 0.6535 (m-70) REVERT: A 153 MET cc_start: 0.0306 (OUTLIER) cc_final: -0.1696 (ttt) REVERT: A 584 ILE cc_start: 0.8221 (mm) cc_final: 0.8007 (mm) REVERT: A 1029 MET cc_start: 0.8683 (tpp) cc_final: 0.8088 (ttp) REVERT: B 780 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: C 360 ASN cc_start: 0.6619 (OUTLIER) cc_final: 0.6393 (p0) REVERT: C 574 ASP cc_start: 0.8346 (p0) cc_final: 0.8120 (p0) REVERT: C 907 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8422 (m-40) REVERT: C 1036 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8725 (tt0) REVERT: C 1132 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8757 (mt) REVERT: H 76 LYS cc_start: 0.5951 (tttm) cc_final: 0.5267 (mtmt) REVERT: H 155 LEU cc_start: 0.1925 (pp) cc_final: 0.1256 (tp) REVERT: I 105 MET cc_start: 0.2056 (ttp) cc_final: 0.0390 (mpp) REVERT: M 6 GLN cc_start: 0.4118 (mt0) cc_final: 0.3266 (tp40) REVERT: M 208 SER cc_start: 0.5468 (OUTLIER) cc_final: 0.4973 (p) REVERT: J 76 LYS cc_start: 0.4552 (tptp) cc_final: 0.3931 (ttmt) REVERT: J 130 THR cc_start: 0.3396 (OUTLIER) cc_final: 0.3077 (m) REVERT: J 196 VAL cc_start: -0.1112 (OUTLIER) cc_final: -0.1701 (t) REVERT: J 215 LYS cc_start: 0.2845 (OUTLIER) cc_final: 0.1599 (mmtp) REVERT: J 228 LYS cc_start: 0.0556 (mttp) cc_final: -0.1619 (tppt) REVERT: N 27 GLN cc_start: 0.0793 (pm20) cc_final: 0.0472 (pt0) REVERT: N 90 GLN cc_start: 0.2774 (pp30) cc_final: 0.2024 (mp10) REVERT: N 103 LYS cc_start: 0.5366 (tptp) cc_final: 0.4653 (mttt) outliers start: 115 outliers final: 71 residues processed: 330 average time/residue: 0.4381 time to fit residues: 246.1957 Evaluate side-chains 281 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 199 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1036 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 TYR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 281 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 325 optimal weight: 7.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 317 ASN A 764 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C1005 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 GLN ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.7757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35426 Z= 0.179 Angle : 0.629 16.321 48186 Z= 0.308 Chirality : 0.046 0.462 5670 Planarity : 0.004 0.053 6137 Dihedral : 6.655 59.256 6155 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.13 % Favored : 92.76 % Rotamer: Outliers : 3.12 % Allowed : 23.78 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.13), residues: 4280 helix: 1.38 (0.21), residues: 692 sheet: -0.21 (0.14), residues: 1323 loop : -1.92 (0.12), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.006 0.001 HIS I 214 PHE 0.017 0.001 PHE A 643 TYR 0.028 0.001 TYR C 495 ARG 0.014 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 206 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7100 (OUTLIER) cc_final: 0.6559 (m-70) REVERT: A 111 ASP cc_start: 0.5527 (OUTLIER) cc_final: 0.5230 (m-30) REVERT: A 153 MET cc_start: 0.0328 (OUTLIER) cc_final: -0.1677 (ttt) REVERT: A 161 SER cc_start: 0.6591 (OUTLIER) cc_final: 0.6367 (p) REVERT: A 584 ILE cc_start: 0.8289 (mm) cc_final: 0.8074 (mm) REVERT: B 780 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: C 574 ASP cc_start: 0.8336 (p0) cc_final: 0.8118 (p0) REVERT: C 1036 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8726 (tt0) REVERT: C 1132 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8765 (mt) REVERT: H 76 LYS cc_start: 0.5978 (tttm) cc_final: 0.5334 (mtmt) REVERT: H 124 THR cc_start: 0.3746 (OUTLIER) cc_final: 0.3360 (p) REVERT: H 155 LEU cc_start: 0.1950 (pp) cc_final: 0.1283 (tp) REVERT: I 59 TYR cc_start: 0.4213 (m-80) cc_final: 0.3865 (m-80) REVERT: I 105 MET cc_start: 0.2017 (ttp) cc_final: 0.0333 (mpp) REVERT: M 6 GLN cc_start: 0.4140 (mt0) cc_final: 0.3272 (tp40) REVERT: M 208 SER cc_start: 0.5457 (OUTLIER) cc_final: 0.4992 (p) REVERT: J 130 THR cc_start: 0.3388 (OUTLIER) cc_final: 0.3059 (m) REVERT: J 196 VAL cc_start: -0.1125 (OUTLIER) cc_final: -0.1674 (t) REVERT: J 228 LYS cc_start: 0.0483 (mttp) cc_final: -0.1626 (tppt) REVERT: N 27 GLN cc_start: 0.0767 (pm20) cc_final: 0.0469 (pt0) REVERT: N 90 GLN cc_start: 0.2744 (pp30) cc_final: 0.1991 (mp10) REVERT: N 103 LYS cc_start: 0.5394 (tptp) cc_final: 0.4667 (mttt) outliers start: 118 outliers final: 88 residues processed: 313 average time/residue: 0.4372 time to fit residues: 231.6777 Evaluate side-chains 294 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 195 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1036 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 TYR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain N residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 9.9990 chunk 396 optimal weight: 20.0000 chunk 361 optimal weight: 10.0000 chunk 385 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 167 optimal weight: 0.8980 chunk 302 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 348 optimal weight: 8.9990 chunk 364 optimal weight: 7.9990 chunk 383 optimal weight: 7.9990 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 370 ASN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 856 ASN C1005 GLN ** I 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.8256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.110 35426 Z= 0.607 Angle : 0.873 15.344 48186 Z= 0.432 Chirality : 0.057 0.507 5670 Planarity : 0.006 0.067 6137 Dihedral : 8.293 59.788 6153 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.88 % Favored : 90.00 % Rotamer: Outliers : 3.78 % Allowed : 23.26 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.83 (0.12), residues: 4280 helix: 0.45 (0.20), residues: 695 sheet: -0.61 (0.14), residues: 1335 loop : -2.20 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP H 117 HIS 0.010 0.002 HIS B1064 PHE 0.032 0.003 PHE A 486 TYR 0.036 0.003 TYR C 495 ARG 0.008 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 199 time to evaluate : 3.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7301 (OUTLIER) cc_final: 0.6818 (m-70) REVERT: A 153 MET cc_start: 0.0850 (OUTLIER) cc_final: 0.0559 (mtm) REVERT: A 161 SER cc_start: 0.6937 (OUTLIER) cc_final: 0.6704 (p) REVERT: A 364 ASP cc_start: 0.6298 (OUTLIER) cc_final: 0.5568 (t0) REVERT: B 497 PHE cc_start: 0.4305 (m-80) cc_final: 0.4008 (m-80) REVERT: B 780 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: C 1036 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8905 (tt0) REVERT: C 1091 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7826 (mtt-85) REVERT: C 1132 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8914 (mt) REVERT: H 76 LYS cc_start: 0.6069 (tttm) cc_final: 0.5412 (mtmt) REVERT: H 124 THR cc_start: 0.3606 (OUTLIER) cc_final: 0.3332 (p) REVERT: I 80 TYR cc_start: 0.3902 (m-80) cc_final: 0.3030 (m-80) REVERT: M 6 GLN cc_start: 0.4175 (mt0) cc_final: 0.3107 (tp40) REVERT: M 208 SER cc_start: 0.5363 (OUTLIER) cc_final: 0.4904 (p) REVERT: J 130 THR cc_start: 0.2914 (OUTLIER) cc_final: 0.2574 (m) REVERT: J 196 VAL cc_start: -0.0839 (OUTLIER) cc_final: -0.1258 (t) REVERT: J 215 LYS cc_start: 0.3019 (OUTLIER) cc_final: 0.1441 (ptmt) REVERT: N 27 GLN cc_start: 0.1088 (pm20) cc_final: 0.0736 (pt0) REVERT: N 90 GLN cc_start: 0.2891 (pp30) cc_final: 0.1970 (mp10) REVERT: N 103 LYS cc_start: 0.5263 (tptp) cc_final: 0.4744 (mttt) outliers start: 143 outliers final: 105 residues processed: 328 average time/residue: 0.4334 time to fit residues: 243.3364 Evaluate side-chains 307 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 189 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1036 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 TYR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain N residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 2.9990 chunk 407 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 193 optimal weight: 4.9990 chunk 283 optimal weight: 6.9990 chunk 427 optimal weight: 30.0000 chunk 393 optimal weight: 10.0000 chunk 340 optimal weight: 40.0000 chunk 35 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 208 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 658 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN I 185 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN N 37 GLN N 90 GLN N 93 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.8368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 35426 Z= 0.320 Angle : 0.712 17.667 48186 Z= 0.351 Chirality : 0.049 0.498 5670 Planarity : 0.005 0.060 6137 Dihedral : 7.631 59.842 6153 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.90 % Favored : 92.01 % Rotamer: Outliers : 3.12 % Allowed : 24.05 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.12), residues: 4280 helix: 0.75 (0.20), residues: 697 sheet: -0.55 (0.14), residues: 1326 loop : -2.19 (0.12), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 117 HIS 0.005 0.001 HIS B1048 PHE 0.022 0.002 PHE A 643 TYR 0.053 0.002 TYR N 36 ARG 0.010 0.001 ARG A 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 197 time to evaluate : 3.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7168 (OUTLIER) cc_final: 0.6689 (m-70) REVERT: A 111 ASP cc_start: 0.5586 (OUTLIER) cc_final: 0.5170 (m-30) REVERT: A 161 SER cc_start: 0.6780 (OUTLIER) cc_final: 0.6538 (p) REVERT: A 364 ASP cc_start: 0.6453 (OUTLIER) cc_final: 0.5799 (t0) REVERT: A 568 ASP cc_start: 0.7352 (p0) cc_final: 0.7086 (p0) REVERT: B 497 PHE cc_start: 0.4252 (m-80) cc_final: 0.3931 (m-80) REVERT: B 780 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: C 1036 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8774 (tt0) REVERT: C 1091 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7811 (mtt-85) REVERT: H 76 LYS cc_start: 0.5984 (tttm) cc_final: 0.5395 (mtmt) REVERT: H 124 THR cc_start: 0.3983 (OUTLIER) cc_final: 0.3686 (p) REVERT: H 155 LEU cc_start: 0.1929 (OUTLIER) cc_final: 0.1241 (tp) REVERT: M 6 GLN cc_start: 0.4287 (mt0) cc_final: 0.3342 (tp40) REVERT: M 208 SER cc_start: 0.5427 (OUTLIER) cc_final: 0.4988 (p) REVERT: J 116 TYR cc_start: 0.2117 (m-80) cc_final: 0.1517 (m-80) REVERT: J 130 THR cc_start: 0.3358 (OUTLIER) cc_final: 0.3022 (m) REVERT: J 196 VAL cc_start: -0.1257 (OUTLIER) cc_final: -0.1706 (t) REVERT: J 211 ASN cc_start: 0.2246 (OUTLIER) cc_final: 0.1668 (t0) REVERT: J 215 LYS cc_start: 0.3151 (OUTLIER) cc_final: 0.1782 (mmtt) REVERT: N 27 GLN cc_start: 0.0755 (pm20) cc_final: 0.0359 (pt0) REVERT: N 36 TYR cc_start: 0.1889 (m-10) cc_final: 0.1389 (m-80) REVERT: N 90 GLN cc_start: 0.2894 (OUTLIER) cc_final: 0.2010 (mp10) REVERT: N 103 LYS cc_start: 0.5341 (tptp) cc_final: 0.4721 (mttt) outliers start: 118 outliers final: 93 residues processed: 301 average time/residue: 0.4550 time to fit residues: 234.3505 Evaluate side-chains 294 residues out of total 3784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 186 time to evaluate : 3.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1036 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 TYR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 90 GLN Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 4.9990 chunk 362 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 313 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 340 optimal weight: 40.0000 chunk 142 optimal weight: 40.0000 chunk 350 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.196750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.160104 restraints weight = 57553.073| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.54 r_work: 0.3664 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.8378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.238 35426 Z= 0.373 Angle : 0.815 59.115 48186 Z= 0.422 Chirality : 0.051 0.860 5670 Planarity : 0.005 0.060 6137 Dihedral : 7.629 59.845 6153 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.06 % Favored : 91.85 % Rotamer: Outliers : 3.25 % Allowed : 24.02 % Favored : 72.73 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.12), residues: 4280 helix: 0.76 (0.20), residues: 697 sheet: -0.56 (0.14), residues: 1328 loop : -2.20 (0.12), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 117 HIS 0.006 0.001 HIS B 207 PHE 0.021 0.002 PHE A 643 TYR 0.040 0.002 TYR N 36 ARG 0.011 0.000 ARG B1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7730.44 seconds wall clock time: 141 minutes 58.51 seconds (8518.51 seconds total)