Starting phenix.real_space_refine on Sun Mar 17 10:07:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/03_2024/5wve_6690_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/03_2024/5wve_6690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/03_2024/5wve_6690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/03_2024/5wve_6690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/03_2024/5wve_6690_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/03_2024/5wve_6690_updated.pdb" } resolution = 4.4 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= 0.011 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: 7 Type Number sf(0) Gaussians Fe 7 7.16 5 P 21 5.49 5 Mg 7 5.21 5 S 516 5.16 5 C 49679 2.51 5 N 13585 2.21 5 O 14790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A GLU 528": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A GLU 934": "OE1" <-> "OE2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C GLU 373": "OE1" <-> "OE2" Residue "C GLU 377": "OE1" <-> "OE2" Residue "C GLU 409": "OE1" <-> "OE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C GLU 528": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 570": "OE1" <-> "OE2" Residue "C GLU 575": "OE1" <-> "OE2" Residue "C GLU 648": "OE1" <-> "OE2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "C GLU 934": "OE1" <-> "OE2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E ARG 228": "NH1" <-> "NH2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 308": "OE1" <-> "OE2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E GLU 339": "OE1" <-> "OE2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "E GLU 373": "OE1" <-> "OE2" Residue "E GLU 377": "OE1" <-> "OE2" Residue "E GLU 409": "OE1" <-> "OE2" Residue "E GLU 412": "OE1" <-> "OE2" Residue "E ARG 434": "NH1" <-> "NH2" Residue "E GLU 528": "OE1" <-> "OE2" Residue "E GLU 546": "OE1" <-> "OE2" Residue "E GLU 570": "OE1" <-> "OE2" Residue "E GLU 575": "OE1" <-> "OE2" Residue "E GLU 648": "OE1" <-> "OE2" Residue "E GLU 652": "OE1" <-> "OE2" Residue "E GLU 934": "OE1" <-> "OE2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "G TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G ARG 228": "NH1" <-> "NH2" Residue "G GLU 283": "OE1" <-> "OE2" Residue "G GLU 308": "OE1" <-> "OE2" Residue "G GLU 316": "OE1" <-> "OE2" Residue "G GLU 339": "OE1" <-> "OE2" Residue "G GLU 366": "OE1" <-> "OE2" Residue "G GLU 373": "OE1" <-> "OE2" Residue "G GLU 377": "OE1" <-> "OE2" Residue "G GLU 409": "OE1" <-> "OE2" Residue "G GLU 412": "OE1" <-> "OE2" Residue "G ARG 434": "NH1" <-> "NH2" Residue "G GLU 528": "OE1" <-> "OE2" Residue "G GLU 546": "OE1" <-> "OE2" Residue "G GLU 570": "OE1" <-> "OE2" Residue "G GLU 575": "OE1" <-> "OE2" Residue "G GLU 648": "OE1" <-> "OE2" Residue "G GLU 652": "OE1" <-> "OE2" Residue "G GLU 934": "OE1" <-> "OE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "I TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 166": "OE1" <-> "OE2" Residue "I ARG 228": "NH1" <-> "NH2" Residue "I GLU 283": "OE1" <-> "OE2" Residue "I GLU 308": "OE1" <-> "OE2" Residue "I GLU 316": "OE1" <-> "OE2" Residue "I GLU 339": "OE1" <-> "OE2" Residue "I GLU 366": "OE1" <-> "OE2" Residue "I GLU 373": "OE1" <-> "OE2" Residue "I GLU 377": "OE1" <-> "OE2" Residue "I GLU 409": "OE1" <-> "OE2" Residue "I GLU 412": "OE1" <-> "OE2" Residue "I ARG 434": "NH1" <-> "NH2" Residue "I GLU 528": "OE1" <-> "OE2" Residue "I GLU 546": "OE1" <-> "OE2" Residue "I GLU 570": "OE1" <-> "OE2" Residue "I GLU 575": "OE1" <-> "OE2" Residue "I GLU 648": "OE1" <-> "OE2" Residue "I GLU 652": "OE1" <-> "OE2" Residue "I GLU 934": "OE1" <-> "OE2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "J TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "K TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "K GLU 175": "OE1" <-> "OE2" Residue "K ARG 228": "NH1" <-> "NH2" Residue "K GLU 283": "OE1" <-> "OE2" Residue "K GLU 308": "OE1" <-> "OE2" Residue "K GLU 316": "OE1" <-> "OE2" Residue "K GLU 339": "OE1" <-> "OE2" Residue "K GLU 366": "OE1" <-> "OE2" Residue "K GLU 373": "OE1" <-> "OE2" Residue "K GLU 377": "OE1" <-> "OE2" Residue "K GLU 409": "OE1" <-> "OE2" Residue "K GLU 412": "OE1" <-> "OE2" Residue "K ARG 434": "NH1" <-> "NH2" Residue "K GLU 528": "OE1" <-> "OE2" Residue "K GLU 546": "OE1" <-> "OE2" Residue "K GLU 570": "OE1" <-> "OE2" Residue "K GLU 575": "OE1" <-> "OE2" Residue "K GLU 648": "OE1" <-> "OE2" Residue "K GLU 652": "OE1" <-> "OE2" Residue "K GLU 934": "OE1" <-> "OE2" Residue "L ARG 38": "NH1" <-> "NH2" Residue "L TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "M TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 166": "OE1" <-> "OE2" Residue "M ARG 228": "NH1" <-> "NH2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M GLU 308": "OE1" <-> "OE2" Residue "M GLU 316": "OE1" <-> "OE2" Residue "M GLU 339": "OE1" <-> "OE2" Residue "M GLU 366": "OE1" <-> "OE2" Residue "M GLU 373": "OE1" <-> "OE2" Residue "M GLU 377": "OE1" <-> "OE2" Residue "M GLU 409": "OE1" <-> "OE2" Residue "M GLU 412": "OE1" <-> "OE2" Residue "M ARG 434": "NH1" <-> "NH2" Residue "M GLU 528": "OE1" <-> "OE2" Residue "M GLU 546": "OE1" <-> "OE2" Residue "M GLU 570": "OE1" <-> "OE2" Residue "M GLU 575": "OE1" <-> "OE2" Residue "M GLU 648": "OE1" <-> "OE2" Residue "M GLU 652": "OE1" <-> "OE2" Residue "M GLU 934": "OE1" <-> "OE2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 62": "OE1" <-> "OE2" Residue "S ARG 45": "NH1" <-> "NH2" Residue "T ARG 36": "NH1" <-> "NH2" Residue "W GLU 14": "OE1" <-> "OE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "X ARG 52": "NH1" <-> "NH2" Residue "Y GLU 3": "OE1" <-> "OE2" Residue "Y ARG 13": "NH1" <-> "NH2" Residue "Y GLU 33": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y ARG 90": "NH1" <-> "NH2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 78605 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 9139 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 28, 'TRANS': 1115} Chain: "B" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 823 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "C" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 9139 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 28, 'TRANS': 1115} Chain: "D" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 823 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "E" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 9139 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 28, 'TRANS': 1115} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 823 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "G" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 9139 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 28, 'TRANS': 1115} Chain: "H" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 823 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "I" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 9139 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 28, 'TRANS': 1115} Chain: "J" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 823 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "K" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 9139 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 28, 'TRANS': 1115} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 823 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "M" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 9139 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 28, 'TRANS': 1115} Chain: "N" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 823 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "O" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "P" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "Q" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "R" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "S" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 762 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "X" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 742 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "Y" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 31.20, per 1000 atoms: 0.40 Number of scatterers: 78605 At special positions: 0 Unit cell: (302.84, 308.2, 148.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 7 26.01 S 516 16.00 P 21 15.00 Mg 7 11.99 O 14790 8.00 N 13585 7.00 C 49679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 663 " distance=2.20 Simple disulfide: pdb=" SG CYS A 675 " - pdb=" SG CYS A 705 " distance=2.02 Simple disulfide: pdb=" SG CYS A 704 " - pdb=" SG CYS A 749 " distance=1.89 Simple disulfide: pdb=" SG CYS A 761 " - pdb=" SG CYS A 804 " distance=2.05 Simple disulfide: pdb=" SG CYS A 803 " - pdb=" SG CYS A 846 " distance=2.09 Simple disulfide: pdb=" SG CYS C 633 " - pdb=" SG CYS C 663 " distance=2.20 Simple disulfide: pdb=" SG CYS C 675 " - pdb=" SG CYS C 705 " distance=2.02 Simple disulfide: pdb=" SG CYS C 704 " - pdb=" SG CYS C 749 " distance=1.89 Simple disulfide: pdb=" SG CYS C 761 " - pdb=" SG CYS C 804 " distance=2.05 Simple disulfide: pdb=" SG CYS C 803 " - pdb=" SG CYS C 846 " distance=2.09 Simple disulfide: pdb=" SG CYS E 633 " - pdb=" SG CYS E 663 " distance=2.20 Simple disulfide: pdb=" SG CYS E 675 " - pdb=" SG CYS E 705 " distance=2.02 Simple disulfide: pdb=" SG CYS E 704 " - pdb=" SG CYS E 749 " distance=1.89 Simple disulfide: pdb=" SG CYS E 761 " - pdb=" SG CYS E 804 " distance=2.05 Simple disulfide: pdb=" SG CYS E 803 " - pdb=" SG CYS E 846 " distance=2.09 Simple disulfide: pdb=" SG CYS G 633 " - pdb=" SG CYS G 663 " distance=2.20 Simple disulfide: pdb=" SG CYS G 675 " - pdb=" SG CYS G 705 " distance=2.02 Simple disulfide: pdb=" SG CYS G 704 " - pdb=" SG CYS G 749 " distance=1.89 Simple disulfide: pdb=" SG CYS G 761 " - pdb=" SG CYS G 804 " distance=2.05 Simple disulfide: pdb=" SG CYS G 803 " - pdb=" SG CYS G 846 " distance=2.09 Simple disulfide: pdb=" SG CYS I 633 " - pdb=" SG CYS I 663 " distance=2.20 Simple disulfide: pdb=" SG CYS I 675 " - pdb=" SG CYS I 705 " distance=2.02 Simple disulfide: pdb=" SG CYS I 704 " - pdb=" SG CYS I 749 " distance=1.89 Simple disulfide: pdb=" SG CYS I 761 " - pdb=" SG CYS I 804 " distance=2.05 Simple disulfide: pdb=" SG CYS I 803 " - pdb=" SG CYS I 846 " distance=2.09 Simple disulfide: pdb=" SG CYS K 633 " - pdb=" SG CYS K 663 " distance=2.19 Simple disulfide: pdb=" SG CYS K 675 " - pdb=" SG CYS K 705 " distance=2.02 Simple disulfide: pdb=" SG CYS K 704 " - pdb=" SG CYS K 749 " distance=1.89 Simple disulfide: pdb=" SG CYS K 761 " - pdb=" SG CYS K 804 " distance=2.05 Simple disulfide: pdb=" SG CYS K 803 " - pdb=" SG CYS K 846 " distance=2.09 Simple disulfide: pdb=" SG CYS M 633 " - pdb=" SG CYS M 663 " distance=2.20 Simple disulfide: pdb=" SG CYS M 675 " - pdb=" SG CYS M 705 " distance=2.02 Simple disulfide: pdb=" SG CYS M 704 " - pdb=" SG CYS M 749 " distance=1.89 Simple disulfide: pdb=" SG CYS M 761 " - pdb=" SG CYS M 804 " distance=2.05 Simple disulfide: pdb=" SG CYS M 803 " - pdb=" SG CYS M 846 " distance=2.09 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=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.57 Conformation dependent library (CDL) restraints added in 10.3 seconds 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 297 helices and 126 sheets defined 31.6% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.52 Creating SS restraints... Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 160 through 169 removed outlier: 3.562A pdb=" N VAL A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.528A pdb=" N GLY A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 206 removed outlier: 3.627A pdb=" N MET A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 232 Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 288 through 299 Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.591A pdb=" N HIS A 311 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 314 " --> pdb=" O HIS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 333 removed outlier: 3.831A pdb=" N ASP A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.879A pdb=" N LEU A 342 " --> pdb=" O TRP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.532A pdb=" N MET A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 388 removed outlier: 3.713A pdb=" N ASP A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 408 through 420 removed outlier: 4.149A pdb=" N ASP A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 7.004A pdb=" N SER A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN A 452 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 removed outlier: 4.214A pdb=" N MET A 481 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 484 " --> pdb=" O MET A 481 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 485 " --> pdb=" O TYR A 482 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE A 486 " --> pdb=" O TRP A 483 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 488 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 491 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 503 Processing helix chain 'A' and resid 507 through 517 Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.536A pdb=" N GLU A 528 " --> pdb=" O HIS A 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 549 removed outlier: 3.665A pdb=" N VAL A 540 " --> pdb=" O LYS A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 No H-bonds generated for 'chain 'A' and resid 551 through 554' Processing helix chain 'A' and resid 563 through 566 No H-bonds generated for 'chain 'A' and resid 563 through 566' Processing helix chain 'A' and resid 574 through 590 removed outlier: 3.555A pdb=" N LEU A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A 589 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN A 590 " --> pdb=" O GLN A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 911 through 915 removed outlier: 4.139A pdb=" N CYS A 915 " --> pdb=" O THR A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 911 through 915' Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 50 through 54 Processing helix chain 'B' and resid 61 through 69 removed outlier: 3.523A pdb=" N GLU B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 88 through 101 Processing helix chain 'C' and resid 108 through 117 Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 160 through 169 removed outlier: 3.562A pdb=" N VAL C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 removed outlier: 3.526A pdb=" N GLY C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 206 removed outlier: 3.627A pdb=" N MET C 197 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 Processing helix chain 'C' and resid 248 through 253 Processing helix chain 'C' and resid 288 through 299 Processing helix chain 'C' and resid 308 through 317 removed outlier: 3.592A pdb=" N HIS C 311 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 314 " --> pdb=" O HIS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 removed outlier: 3.829A pdb=" N ASP C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 347 removed outlier: 3.879A pdb=" N LEU C 342 " --> pdb=" O TRP C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 374 removed outlier: 3.530A pdb=" N MET C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE C 370 " --> pdb=" O GLU C 366 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 388 removed outlier: 3.713A pdb=" N ASP C 381 " --> pdb=" O GLU C 377 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR C 382 " --> pdb=" O ASP C 378 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP C 385 " --> pdb=" O ASP C 381 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE C 388 " --> pdb=" O THR C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 404 Processing helix chain 'C' and resid 408 through 420 removed outlier: 4.149A pdb=" N ASP C 413 " --> pdb=" O GLU C 409 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE C 414 " --> pdb=" O GLU C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 466 removed outlier: 7.003A pdb=" N SER C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN C 452 " --> pdb=" O LYS C 448 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN C 454 " --> pdb=" O CYS C 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP C 455 " --> pdb=" O SER C 451 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 463 " --> pdb=" O LYS C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 494 removed outlier: 4.214A pdb=" N MET C 481 " --> pdb=" O GLU C 478 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 484 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 485 " --> pdb=" O TYR C 482 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE C 486 " --> pdb=" O TRP C 483 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 488 " --> pdb=" O ASN C 485 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET C 491 " --> pdb=" O ALA C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 503 Processing helix chain 'C' and resid 507 through 517 Processing helix chain 'C' and resid 521 through 532 removed outlier: 3.538A pdb=" N GLU C 528 " --> pdb=" O HIS C 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 532 " --> pdb=" O GLU C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 549 removed outlier: 3.667A pdb=" N VAL C 540 " --> pdb=" O LYS C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 No H-bonds generated for 'chain 'C' and resid 551 through 554' Processing helix chain 'C' and resid 563 through 566 No H-bonds generated for 'chain 'C' and resid 563 through 566' Processing helix chain 'C' and resid 574 through 590 removed outlier: 3.554A pdb=" N LEU C 582 " --> pdb=" O GLN C 578 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP C 589 " --> pdb=" O LYS C 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN C 590 " --> pdb=" O GLN C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 602 No H-bonds generated for 'chain 'C' and resid 600 through 602' Processing helix chain 'C' and resid 851 through 853 No H-bonds generated for 'chain 'C' and resid 851 through 853' Processing helix chain 'C' and resid 911 through 915 removed outlier: 4.140A pdb=" N CYS C 915 " --> pdb=" O THR C 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 911 through 915' Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 50 through 54 Processing helix chain 'D' and resid 61 through 69 removed outlier: 3.524A pdb=" N GLU D 69 " --> pdb=" O MET D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 74 No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'D' and resid 88 through 101 Processing helix chain 'E' and resid 108 through 117 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 160 through 169 removed outlier: 3.561A pdb=" N VAL E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 177 removed outlier: 3.527A pdb=" N GLY E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 206 removed outlier: 3.628A pdb=" N MET E 197 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 232 Processing helix chain 'E' and resid 248 through 253 Processing helix chain 'E' and resid 288 through 299 Processing helix chain 'E' and resid 308 through 317 removed outlier: 3.593A pdb=" N HIS E 311 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE E 314 " --> pdb=" O HIS E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 333 removed outlier: 3.831A pdb=" N ASP E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 347 removed outlier: 3.879A pdb=" N LEU E 342 " --> pdb=" O TRP E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 374 removed outlier: 3.532A pdb=" N MET E 368 " --> pdb=" O LEU E 364 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE E 370 " --> pdb=" O GLU E 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU E 373 " --> pdb=" O SER E 369 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET E 374 " --> pdb=" O ILE E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 388 removed outlier: 3.712A pdb=" N ASP E 381 " --> pdb=" O GLU E 377 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR E 382 " --> pdb=" O ASP E 378 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE E 388 " --> pdb=" O THR E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 404 Processing helix chain 'E' and resid 408 through 420 removed outlier: 4.149A pdb=" N ASP E 413 " --> pdb=" O GLU E 409 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 414 " --> pdb=" O GLU E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 466 removed outlier: 7.003A pdb=" N SER E 451 " --> pdb=" O GLU E 447 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN E 452 " --> pdb=" O LYS E 448 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN E 454 " --> pdb=" O CYS E 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP E 455 " --> pdb=" O SER E 451 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS E 458 " --> pdb=" O GLN E 454 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS E 459 " --> pdb=" O ASP E 455 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN E 463 " --> pdb=" O LYS E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 494 removed outlier: 4.216A pdb=" N MET E 481 " --> pdb=" O GLU E 478 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR E 484 " --> pdb=" O MET E 481 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN E 485 " --> pdb=" O TYR E 482 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE E 486 " --> pdb=" O TRP E 483 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA E 488 " --> pdb=" O ASN E 485 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET E 491 " --> pdb=" O ALA E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 503 Processing helix chain 'E' and resid 507 through 517 Processing helix chain 'E' and resid 521 through 532 removed outlier: 3.537A pdb=" N GLU E 528 " --> pdb=" O HIS E 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS E 531 " --> pdb=" O VAL E 527 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE E 532 " --> pdb=" O GLU E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 549 removed outlier: 3.667A pdb=" N VAL E 540 " --> pdb=" O LYS E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 554 No H-bonds generated for 'chain 'E' and resid 551 through 554' Processing helix chain 'E' and resid 563 through 566 No H-bonds generated for 'chain 'E' and resid 563 through 566' Processing helix chain 'E' and resid 574 through 590 removed outlier: 3.554A pdb=" N LEU E 582 " --> pdb=" O GLN E 578 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP E 589 " --> pdb=" O LYS E 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN E 590 " --> pdb=" O GLN E 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 602 No H-bonds generated for 'chain 'E' and resid 600 through 602' Processing helix chain 'E' and resid 851 through 853 No H-bonds generated for 'chain 'E' and resid 851 through 853' Processing helix chain 'E' and resid 911 through 915 removed outlier: 4.141A pdb=" N CYS E 915 " --> pdb=" O THR E 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 911 through 915' Processing helix chain 'F' and resid 3 through 13 Processing helix chain 'F' and resid 50 through 54 Processing helix chain 'F' and resid 61 through 69 removed outlier: 3.524A pdb=" N GLU F 69 " --> pdb=" O MET F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 74 No H-bonds generated for 'chain 'F' and resid 71 through 74' Processing helix chain 'F' and resid 88 through 101 Processing helix chain 'G' and resid 108 through 117 Processing helix chain 'G' and resid 130 through 142 Processing helix chain 'G' and resid 160 through 169 removed outlier: 3.562A pdb=" N VAL G 168 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 177 removed outlier: 3.526A pdb=" N GLY G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 206 removed outlier: 3.627A pdb=" N MET G 197 " --> pdb=" O SER G 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS G 198 " --> pdb=" O GLY G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 232 Processing helix chain 'G' and resid 248 through 253 Processing helix chain 'G' and resid 288 through 299 Processing helix chain 'G' and resid 308 through 317 removed outlier: 3.593A pdb=" N HIS G 311 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE G 314 " --> pdb=" O HIS G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 333 removed outlier: 3.830A pdb=" N ASP G 333 " --> pdb=" O ALA G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 347 removed outlier: 3.879A pdb=" N LEU G 342 " --> pdb=" O TRP G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 374 removed outlier: 3.532A pdb=" N MET G 368 " --> pdb=" O LEU G 364 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE G 370 " --> pdb=" O GLU G 366 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU G 373 " --> pdb=" O SER G 369 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET G 374 " --> pdb=" O ILE G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 388 removed outlier: 3.712A pdb=" N ASP G 381 " --> pdb=" O GLU G 377 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR G 382 " --> pdb=" O ASP G 378 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR G 384 " --> pdb=" O LYS G 380 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP G 385 " --> pdb=" O ASP G 381 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE G 388 " --> pdb=" O THR G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 404 Processing helix chain 'G' and resid 408 through 420 removed outlier: 4.148A pdb=" N ASP G 413 " --> pdb=" O GLU G 409 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE G 414 " --> pdb=" O GLU G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 466 removed outlier: 7.003A pdb=" N SER G 451 " --> pdb=" O GLU G 447 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN G 452 " --> pdb=" O LYS G 448 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN G 454 " --> pdb=" O CYS G 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP G 455 " --> pdb=" O SER G 451 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS G 458 " --> pdb=" O GLN G 454 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS G 459 " --> pdb=" O ASP G 455 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN G 463 " --> pdb=" O LYS G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 494 removed outlier: 4.215A pdb=" N MET G 481 " --> pdb=" O GLU G 478 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR G 484 " --> pdb=" O MET G 481 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN G 485 " --> pdb=" O TYR G 482 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE G 486 " --> pdb=" O TRP G 483 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA G 488 " --> pdb=" O ASN G 485 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET G 491 " --> pdb=" O ALA G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 503 Processing helix chain 'G' and resid 507 through 517 Processing helix chain 'G' and resid 521 through 532 removed outlier: 3.537A pdb=" N GLU G 528 " --> pdb=" O HIS G 524 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS G 531 " --> pdb=" O VAL G 527 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE G 532 " --> pdb=" O GLU G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 535 through 549 removed outlier: 3.666A pdb=" N VAL G 540 " --> pdb=" O LYS G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 554 No H-bonds generated for 'chain 'G' and resid 551 through 554' Processing helix chain 'G' and resid 563 through 566 No H-bonds generated for 'chain 'G' and resid 563 through 566' Processing helix chain 'G' and resid 574 through 590 removed outlier: 3.553A pdb=" N LEU G 582 " --> pdb=" O GLN G 578 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP G 589 " --> pdb=" O LYS G 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN G 590 " --> pdb=" O GLN G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 600 through 602 No H-bonds generated for 'chain 'G' and resid 600 through 602' Processing helix chain 'G' and resid 851 through 853 No H-bonds generated for 'chain 'G' and resid 851 through 853' Processing helix chain 'G' and resid 911 through 915 removed outlier: 4.140A pdb=" N CYS G 915 " --> pdb=" O THR G 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 911 through 915' Processing helix chain 'H' and resid 3 through 13 Processing helix chain 'H' and resid 50 through 54 Processing helix chain 'H' and resid 61 through 69 removed outlier: 3.523A pdb=" N GLU H 69 " --> pdb=" O MET H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 74 No H-bonds generated for 'chain 'H' and resid 71 through 74' Processing helix chain 'H' and resid 88 through 101 Processing helix chain 'I' and resid 108 through 117 Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 160 through 169 removed outlier: 3.561A pdb=" N VAL I 168 " --> pdb=" O ALA I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 177 removed outlier: 3.526A pdb=" N GLY I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 206 removed outlier: 3.628A pdb=" N MET I 197 " --> pdb=" O SER I 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS I 198 " --> pdb=" O GLY I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 232 Processing helix chain 'I' and resid 248 through 253 Processing helix chain 'I' and resid 288 through 299 Processing helix chain 'I' and resid 308 through 317 removed outlier: 3.593A pdb=" N HIS I 311 " --> pdb=" O GLU I 308 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE I 314 " --> pdb=" O HIS I 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 333 removed outlier: 3.832A pdb=" N ASP I 333 " --> pdb=" O ALA I 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 347 removed outlier: 3.879A pdb=" N LEU I 342 " --> pdb=" O TRP I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 374 removed outlier: 3.532A pdb=" N MET I 368 " --> pdb=" O LEU I 364 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE I 370 " --> pdb=" O GLU I 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU I 373 " --> pdb=" O SER I 369 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET I 374 " --> pdb=" O ILE I 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 388 removed outlier: 3.713A pdb=" N ASP I 381 " --> pdb=" O GLU I 377 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR I 382 " --> pdb=" O ASP I 378 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR I 384 " --> pdb=" O LYS I 380 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP I 385 " --> pdb=" O ASP I 381 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE I 388 " --> pdb=" O THR I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 404 Processing helix chain 'I' and resid 408 through 420 removed outlier: 4.149A pdb=" N ASP I 413 " --> pdb=" O GLU I 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE I 414 " --> pdb=" O GLU I 410 " (cutoff:3.500A) Processing helix chain 'I' and resid 439 through 466 removed outlier: 7.001A pdb=" N SER I 451 " --> pdb=" O GLU I 447 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN I 452 " --> pdb=" O LYS I 448 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN I 454 " --> pdb=" O CYS I 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP I 455 " --> pdb=" O SER I 451 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS I 458 " --> pdb=" O GLN I 454 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS I 459 " --> pdb=" O ASP I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 494 removed outlier: 4.213A pdb=" N MET I 481 " --> pdb=" O GLU I 478 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR I 484 " --> pdb=" O MET I 481 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN I 485 " --> pdb=" O TYR I 482 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE I 486 " --> pdb=" O TRP I 483 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA I 488 " --> pdb=" O ASN I 485 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET I 491 " --> pdb=" O ALA I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 503 Processing helix chain 'I' and resid 507 through 517 Processing helix chain 'I' and resid 521 through 532 removed outlier: 3.539A pdb=" N GLU I 528 " --> pdb=" O HIS I 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS I 531 " --> pdb=" O VAL I 527 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE I 532 " --> pdb=" O GLU I 528 " (cutoff:3.500A) Processing helix chain 'I' and resid 535 through 549 removed outlier: 3.666A pdb=" N VAL I 540 " --> pdb=" O LYS I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 554 No H-bonds generated for 'chain 'I' and resid 551 through 554' Processing helix chain 'I' and resid 563 through 566 No H-bonds generated for 'chain 'I' and resid 563 through 566' Processing helix chain 'I' and resid 574 through 590 removed outlier: 3.553A pdb=" N LEU I 582 " --> pdb=" O GLN I 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP I 589 " --> pdb=" O LYS I 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN I 590 " --> pdb=" O GLN I 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 600 through 602 No H-bonds generated for 'chain 'I' and resid 600 through 602' Processing helix chain 'I' and resid 851 through 853 No H-bonds generated for 'chain 'I' and resid 851 through 853' Processing helix chain 'I' and resid 911 through 915 removed outlier: 4.141A pdb=" N CYS I 915 " --> pdb=" O THR I 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 911 through 915' Processing helix chain 'J' and resid 3 through 13 Processing helix chain 'J' and resid 50 through 54 Processing helix chain 'J' and resid 61 through 69 removed outlier: 3.522A pdb=" N GLU J 69 " --> pdb=" O MET J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 74 No H-bonds generated for 'chain 'J' and resid 71 through 74' Processing helix chain 'J' and resid 88 through 101 Processing helix chain 'K' and resid 108 through 117 Processing helix chain 'K' and resid 130 through 142 Processing helix chain 'K' and resid 160 through 169 removed outlier: 3.563A pdb=" N VAL K 168 " --> pdb=" O ALA K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 177 removed outlier: 3.526A pdb=" N GLY K 176 " --> pdb=" O SER K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 206 removed outlier: 3.626A pdb=" N MET K 197 " --> pdb=" O SER K 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS K 198 " --> pdb=" O GLY K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 232 Processing helix chain 'K' and resid 248 through 253 Processing helix chain 'K' and resid 288 through 299 Processing helix chain 'K' and resid 308 through 317 removed outlier: 3.593A pdb=" N HIS K 311 " --> pdb=" O GLU K 308 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE K 314 " --> pdb=" O HIS K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 333 removed outlier: 3.832A pdb=" N ASP K 333 " --> pdb=" O ALA K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 347 removed outlier: 3.878A pdb=" N LEU K 342 " --> pdb=" O TRP K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 364 through 374 removed outlier: 3.532A pdb=" N MET K 368 " --> pdb=" O LEU K 364 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE K 370 " --> pdb=" O GLU K 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU K 373 " --> pdb=" O SER K 369 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N MET K 374 " --> pdb=" O ILE K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 388 removed outlier: 3.711A pdb=" N ASP K 381 " --> pdb=" O GLU K 377 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR K 382 " --> pdb=" O ASP K 378 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR K 384 " --> pdb=" O LYS K 380 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP K 385 " --> pdb=" O ASP K 381 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE K 388 " --> pdb=" O THR K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 404 Processing helix chain 'K' and resid 408 through 420 removed outlier: 4.148A pdb=" N ASP K 413 " --> pdb=" O GLU K 409 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE K 414 " --> pdb=" O GLU K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 439 through 466 removed outlier: 7.004A pdb=" N SER K 451 " --> pdb=" O GLU K 447 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN K 452 " --> pdb=" O LYS K 448 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN K 454 " --> pdb=" O CYS K 450 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP K 455 " --> pdb=" O SER K 451 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS K 458 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS K 459 " --> pdb=" O ASP K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 494 removed outlier: 4.214A pdb=" N MET K 481 " --> pdb=" O GLU K 478 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR K 484 " --> pdb=" O MET K 481 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN K 485 " --> pdb=" O TYR K 482 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE K 486 " --> pdb=" O TRP K 483 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA K 488 " --> pdb=" O ASN K 485 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET K 491 " --> pdb=" O ALA K 488 " (cutoff:3.500A) Processing helix chain 'K' and resid 497 through 503 Processing helix chain 'K' and resid 507 through 517 Processing helix chain 'K' and resid 521 through 532 removed outlier: 3.538A pdb=" N GLU K 528 " --> pdb=" O HIS K 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS K 531 " --> pdb=" O VAL K 527 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE K 532 " --> pdb=" O GLU K 528 " (cutoff:3.500A) Processing helix chain 'K' and resid 535 through 549 removed outlier: 3.666A pdb=" N VAL K 540 " --> pdb=" O LYS K 536 " (cutoff:3.500A) Processing helix chain 'K' and resid 551 through 554 No H-bonds generated for 'chain 'K' and resid 551 through 554' Processing helix chain 'K' and resid 563 through 566 No H-bonds generated for 'chain 'K' and resid 563 through 566' Processing helix chain 'K' and resid 574 through 590 removed outlier: 3.553A pdb=" N LEU K 582 " --> pdb=" O GLN K 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP K 589 " --> pdb=" O LYS K 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN K 590 " --> pdb=" O GLN K 586 " (cutoff:3.500A) Processing helix chain 'K' and resid 600 through 602 No H-bonds generated for 'chain 'K' and resid 600 through 602' Processing helix chain 'K' and resid 851 through 853 No H-bonds generated for 'chain 'K' and resid 851 through 853' Processing helix chain 'K' and resid 911 through 915 removed outlier: 4.141A pdb=" N CYS K 915 " --> pdb=" O THR K 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 911 through 915' Processing helix chain 'L' and resid 3 through 13 Processing helix chain 'L' and resid 50 through 54 Processing helix chain 'L' and resid 61 through 69 removed outlier: 3.523A pdb=" N GLU L 69 " --> pdb=" O MET L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 74 No H-bonds generated for 'chain 'L' and resid 71 through 74' Processing helix chain 'L' and resid 88 through 101 Processing helix chain 'M' and resid 108 through 117 Processing helix chain 'M' and resid 130 through 142 Processing helix chain 'M' and resid 160 through 167 Processing helix chain 'M' and resid 171 through 177 removed outlier: 3.526A pdb=" N GLY M 176 " --> pdb=" O SER M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 206 removed outlier: 3.628A pdb=" N MET M 197 " --> pdb=" O SER M 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS M 198 " --> pdb=" O GLY M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 232 Processing helix chain 'M' and resid 248 through 253 Processing helix chain 'M' and resid 288 through 299 Processing helix chain 'M' and resid 308 through 317 removed outlier: 3.590A pdb=" N HIS M 311 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE M 314 " --> pdb=" O HIS M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 333 removed outlier: 3.831A pdb=" N ASP M 333 " --> pdb=" O ALA M 329 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 347 removed outlier: 3.878A pdb=" N LEU M 342 " --> pdb=" O TRP M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 364 through 374 removed outlier: 3.532A pdb=" N MET M 368 " --> pdb=" O LEU M 364 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE M 370 " --> pdb=" O GLU M 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU M 373 " --> pdb=" O SER M 369 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET M 374 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 388 removed outlier: 3.714A pdb=" N ASP M 381 " --> pdb=" O GLU M 377 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR M 382 " --> pdb=" O ASP M 378 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR M 384 " --> pdb=" O LYS M 380 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP M 385 " --> pdb=" O ASP M 381 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE M 388 " --> pdb=" O THR M 384 " (cutoff:3.500A) Processing helix chain 'M' and resid 397 through 404 Processing helix chain 'M' and resid 408 through 420 removed outlier: 4.151A pdb=" N ASP M 413 " --> pdb=" O GLU M 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE M 414 " --> pdb=" O GLU M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 466 removed outlier: 7.004A pdb=" N SER M 451 " --> pdb=" O GLU M 447 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN M 452 " --> pdb=" O LYS M 448 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN M 454 " --> pdb=" O CYS M 450 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP M 455 " --> pdb=" O SER M 451 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS M 458 " --> pdb=" O GLN M 454 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS M 459 " --> pdb=" O ASP M 455 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN M 463 " --> pdb=" O LYS M 459 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 494 removed outlier: 4.215A pdb=" N MET M 481 " --> pdb=" O GLU M 478 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR M 484 " --> pdb=" O MET M 481 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN M 485 " --> pdb=" O TYR M 482 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE M 486 " --> pdb=" O TRP M 483 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA M 488 " --> pdb=" O ASN M 485 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET M 491 " --> pdb=" O ALA M 488 " (cutoff:3.500A) Processing helix chain 'M' and resid 497 through 503 Processing helix chain 'M' and resid 507 through 517 Processing helix chain 'M' and resid 521 through 532 removed outlier: 3.537A pdb=" N GLU M 528 " --> pdb=" O HIS M 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS M 531 " --> pdb=" O VAL M 527 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE M 532 " --> pdb=" O GLU M 528 " (cutoff:3.500A) Processing helix chain 'M' and resid 535 through 549 removed outlier: 3.667A pdb=" N VAL M 540 " --> pdb=" O LYS M 536 " (cutoff:3.500A) Processing helix chain 'M' and resid 551 through 554 No H-bonds generated for 'chain 'M' and resid 551 through 554' Processing helix chain 'M' and resid 563 through 566 No H-bonds generated for 'chain 'M' and resid 563 through 566' Processing helix chain 'M' and resid 574 through 590 removed outlier: 3.552A pdb=" N LEU M 582 " --> pdb=" O GLN M 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP M 589 " --> pdb=" O LYS M 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN M 590 " --> pdb=" O GLN M 586 " (cutoff:3.500A) Processing helix chain 'M' and resid 600 through 602 No H-bonds generated for 'chain 'M' and resid 600 through 602' Processing helix chain 'M' and resid 851 through 853 No H-bonds generated for 'chain 'M' and resid 851 through 853' Processing helix chain 'M' and resid 911 through 915 removed outlier: 4.140A pdb=" N CYS M 915 " --> pdb=" O THR M 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 911 through 915' Processing helix chain 'N' and resid 3 through 13 Processing helix chain 'N' and resid 50 through 54 Processing helix chain 'N' and resid 61 through 69 removed outlier: 3.521A pdb=" N GLU N 69 " --> pdb=" O MET N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 74 No H-bonds generated for 'chain 'N' and resid 71 through 74' Processing helix chain 'N' and resid 88 through 101 Processing helix chain 'O' and resid 3 through 17 removed outlier: 4.962A pdb=" N GLU O 14 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA O 15 " --> pdb=" O GLN O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 32 Processing helix chain 'O' and resid 37 through 44 Processing helix chain 'O' and resid 49 through 62 removed outlier: 4.079A pdb=" N LYS O 62 " --> pdb=" O LYS O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 77 Processing helix chain 'O' and resid 81 through 90 removed outlier: 4.303A pdb=" N ASP O 89 " --> pdb=" O ALA O 85 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLY O 90 " --> pdb=" O LEU O 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 17 removed outlier: 4.962A pdb=" N GLU P 14 " --> pdb=" O LEU P 10 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA P 15 " --> pdb=" O GLN P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 32 Processing helix chain 'P' and resid 37 through 44 Processing helix chain 'P' and resid 49 through 62 removed outlier: 3.976A pdb=" N LYS P 62 " --> pdb=" O LYS P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 77 Processing helix chain 'P' and resid 81 through 90 removed outlier: 4.305A pdb=" N ASP P 89 " --> pdb=" O ALA P 85 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY P 90 " --> pdb=" O LEU P 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 17 removed outlier: 4.962A pdb=" N GLU Q 14 " --> pdb=" O LEU Q 10 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA Q 15 " --> pdb=" O GLN Q 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 32 Processing helix chain 'Q' and resid 37 through 45 Processing helix chain 'Q' and resid 49 through 62 removed outlier: 3.977A pdb=" N LYS Q 62 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 77 Processing helix chain 'Q' and resid 81 through 90 removed outlier: 4.305A pdb=" N ASP Q 89 " --> pdb=" O ALA Q 85 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY Q 90 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 17 removed outlier: 4.962A pdb=" N GLU R 14 " --> pdb=" O LEU R 10 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA R 15 " --> pdb=" O GLN R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 32 Processing helix chain 'R' and resid 37 through 44 Processing helix chain 'R' and resid 49 through 62 removed outlier: 3.977A pdb=" N LYS R 62 " --> pdb=" O LYS R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 77 Processing helix chain 'R' and resid 81 through 90 removed outlier: 4.304A pdb=" N ASP R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLY R 90 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 11 Processing helix chain 'S' and resid 13 through 19 Processing helix chain 'S' and resid 26 through 31 Processing helix chain 'S' and resid 37 through 44 Processing helix chain 'S' and resid 51 through 64 removed outlier: 4.019A pdb=" N GLU S 63 " --> pdb=" O ILE S 59 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR S 64 " --> pdb=" O ILE S 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 80 Processing helix chain 'S' and resid 83 through 94 Processing helix chain 'T' and resid 3 through 11 Processing helix chain 'T' and resid 13 through 19 Processing helix chain 'T' and resid 26 through 31 Processing helix chain 'T' and resid 37 through 44 Processing helix chain 'T' and resid 51 through 64 removed outlier: 4.020A pdb=" N GLU T 63 " --> pdb=" O ILE T 59 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR T 64 " --> pdb=" O ILE T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 80 Processing helix chain 'T' and resid 83 through 94 Processing helix chain 'U' and resid 3 through 11 removed outlier: 3.842A pdb=" N ARG U 10 " --> pdb=" O ARG U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 17 Processing helix chain 'U' and resid 26 through 31 Processing helix chain 'U' and resid 37 through 44 Processing helix chain 'U' and resid 51 through 64 removed outlier: 4.019A pdb=" N GLU U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR U 64 " --> pdb=" O ILE U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 69 through 80 Processing helix chain 'U' and resid 83 through 94 Processing helix chain 'V' and resid 3 through 11 Processing helix chain 'V' and resid 13 through 19 Processing helix chain 'V' and resid 26 through 31 Processing helix chain 'V' and resid 37 through 44 Processing helix chain 'V' and resid 51 through 64 removed outlier: 4.020A pdb=" N GLU V 63 " --> pdb=" O ILE V 59 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR V 64 " --> pdb=" O ILE V 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 69 through 80 Processing helix chain 'V' and resid 83 through 94 Processing helix chain 'W' and resid 3 through 11 Processing helix chain 'W' and resid 13 through 19 Processing helix chain 'W' and resid 22 through 24 No H-bonds generated for 'chain 'W' and resid 22 through 24' Processing helix chain 'W' and resid 26 through 31 Processing helix chain 'W' and resid 37 through 44 Processing helix chain 'W' and resid 49 through 62 removed outlier: 4.001A pdb=" N LYS W 62 " --> pdb=" O LYS W 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 77 Processing helix chain 'W' and resid 81 through 90 removed outlier: 4.651A pdb=" N ASP W 89 " --> pdb=" O ALA W 85 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLY W 90 " --> pdb=" O LEU W 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 19 removed outlier: 5.133A pdb=" N GLU X 14 " --> pdb=" O LEU X 10 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA X 15 " --> pdb=" O GLN X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 22 through 32 Processing helix chain 'X' and resid 37 through 45 Processing helix chain 'X' and resid 49 through 62 removed outlier: 3.633A pdb=" N LYS X 62 " --> pdb=" O LYS X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 65 through 77 Processing helix chain 'X' and resid 81 through 90 removed outlier: 4.115A pdb=" N ASP X 89 " --> pdb=" O ALA X 85 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLY X 90 " --> pdb=" O LEU X 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 11 Processing helix chain 'Y' and resid 13 through 19 Processing helix chain 'Y' and resid 26 through 31 Processing helix chain 'Y' and resid 37 through 44 Processing helix chain 'Y' and resid 51 through 64 removed outlier: 3.719A pdb=" N GLU Y 63 " --> pdb=" O ILE Y 59 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR Y 64 " --> pdb=" O ILE Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 80 Processing helix chain 'Y' and resid 83 through 93 removed outlier: 3.755A pdb=" N ASN Y 92 " --> pdb=" O PHE Y 88 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 277 through 281 removed outlier: 6.770A pdb=" N TRP A 149 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL A 280 " --> pdb=" O TRP A 149 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR A 151 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE A 260 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ILE A 152 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU A 262 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU A 240 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR A 263 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU A 242 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 609 through 611 removed outlier: 3.902A pdb=" N LEU A 609 " --> pdb=" O LEU A 908 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 621 through 623 removed outlier: 6.330A pdb=" N LYS A 643 " --> pdb=" O LYS A 649 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS A 649 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY A 719 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS A 705 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA A 717 " --> pdb=" O CYS A 705 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE A 707 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 715 " --> pdb=" O PHE A 707 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP A 729 " --> pdb=" O CYS A 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS A 735 " --> pdb=" O ASP A 729 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 768 through 771 removed outlier: 3.847A pdb=" N HIS A 748 " --> pdb=" O CYS A 761 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 804 through 806 removed outlier: 5.463A pdb=" N ASP A 825 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU A 831 " --> pdb=" O ASP A 825 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 854 through 858 removed outlier: 5.505A pdb=" N ASN A 868 " --> pdb=" O LYS A 874 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS A 874 " --> pdb=" O ASN A 868 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 928 through 930 removed outlier: 3.790A pdb=" N MET A 936 " --> pdb=" O VAL A 929 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 967 through 969 Processing sheet with id= J, first strand: chain 'A' and resid 1009 through 1011 Processing sheet with id= K, first strand: chain 'A' and resid 1079 through 1081 Processing sheet with id= L, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 3.515A pdb=" N SER A1090 " --> pdb=" O SER A1104 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1132 through 1135 Processing sheet with id= N, first strand: chain 'A' and resid 1182 through 1185 removed outlier: 4.000A pdb=" N ASP A1182 " --> pdb=" O ALA A1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A1195 " --> pdb=" O ASP A1182 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 1233 through 1235 Processing sheet with id= P, first strand: chain 'A' and resid 660 through 665 removed outlier: 6.642A pdb=" N CYS A 675 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N CYS A 663 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA A 673 " --> pdb=" O CYS A 663 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 681 through 684 Processing sheet with id= R, first strand: chain 'A' and resid 885 through 890 removed outlier: 6.366A pdb=" N SER A 900 " --> pdb=" O HIS A 886 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A 888 " --> pdb=" O LEU A 898 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 898 " --> pdb=" O VAL A 888 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 277 through 281 removed outlier: 6.770A pdb=" N TRP C 149 " --> pdb=" O TYR C 278 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL C 280 " --> pdb=" O TRP C 149 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR C 151 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE C 260 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N ILE C 152 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU C 262 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU C 240 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR C 263 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU C 242 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 609 through 611 removed outlier: 3.902A pdb=" N LEU C 609 " --> pdb=" O LEU C 908 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 621 through 623 removed outlier: 6.328A pdb=" N LYS C 643 " --> pdb=" O LYS C 649 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS C 649 " --> pdb=" O LYS C 643 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY C 719 " --> pdb=" O ASN C 703 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N CYS C 705 " --> pdb=" O ALA C 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA C 717 " --> pdb=" O CYS C 705 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE C 707 " --> pdb=" O LEU C 715 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 715 " --> pdb=" O PHE C 707 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP C 729 " --> pdb=" O CYS C 735 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N CYS C 735 " --> pdb=" O ASP C 729 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 768 through 771 removed outlier: 3.845A pdb=" N HIS C 748 " --> pdb=" O CYS C 761 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 804 through 806 removed outlier: 5.463A pdb=" N ASP C 825 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU C 831 " --> pdb=" O ASP C 825 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 854 through 858 removed outlier: 5.505A pdb=" N ASN C 868 " --> pdb=" O LYS C 874 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS C 874 " --> pdb=" O ASN C 868 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 928 through 930 removed outlier: 3.792A pdb=" N MET C 936 " --> pdb=" O VAL C 929 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 967 through 969 Processing sheet with id= AB, first strand: chain 'C' and resid 1009 through 1011 Processing sheet with id= AC, first strand: chain 'C' and resid 1079 through 1081 Processing sheet with id= AD, first strand: chain 'C' and resid 1090 through 1093 removed outlier: 3.516A pdb=" N SER C1090 " --> pdb=" O SER C1104 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 1132 through 1135 Processing sheet with id= AF, first strand: chain 'C' and resid 1182 through 1185 removed outlier: 4.002A pdb=" N ASP C1182 " --> pdb=" O ALA C1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C1195 " --> pdb=" O ASP C1182 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 1233 through 1235 Processing sheet with id= AH, first strand: chain 'C' and resid 660 through 665 removed outlier: 6.642A pdb=" N CYS C 675 " --> pdb=" O LEU C 661 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS C 663 " --> pdb=" O ALA C 673 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA C 673 " --> pdb=" O CYS C 663 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 681 through 684 Processing sheet with id= AJ, first strand: chain 'C' and resid 885 through 890 removed outlier: 6.367A pdb=" N SER C 900 " --> pdb=" O HIS C 886 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL C 888 " --> pdb=" O LEU C 898 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 898 " --> pdb=" O VAL C 888 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 277 through 281 removed outlier: 6.771A pdb=" N TRP E 149 " --> pdb=" O TYR E 278 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL E 280 " --> pdb=" O TRP E 149 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR E 151 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE E 260 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ILE E 152 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU E 262 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU E 240 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR E 263 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU E 242 " --> pdb=" O THR E 263 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 609 through 611 removed outlier: 3.903A pdb=" N LEU E 609 " --> pdb=" O LEU E 908 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 621 through 623 removed outlier: 6.327A pdb=" N LYS E 643 " --> pdb=" O LYS E 649 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS E 649 " --> pdb=" O LYS E 643 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'E' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY E 719 " --> pdb=" O ASN E 703 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS E 705 " --> pdb=" O ALA E 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA E 717 " --> pdb=" O CYS E 705 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE E 707 " --> pdb=" O LEU E 715 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU E 715 " --> pdb=" O PHE E 707 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP E 729 " --> pdb=" O CYS E 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS E 735 " --> pdb=" O ASP E 729 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'E' and resid 768 through 771 removed outlier: 3.846A pdb=" N HIS E 748 " --> pdb=" O CYS E 761 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'E' and resid 804 through 806 removed outlier: 5.463A pdb=" N ASP E 825 " --> pdb=" O LEU E 831 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU E 831 " --> pdb=" O ASP E 825 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'E' and resid 854 through 858 removed outlier: 5.506A pdb=" N ASN E 868 " --> pdb=" O LYS E 874 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LYS E 874 " --> pdb=" O ASN E 868 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'E' and resid 928 through 930 removed outlier: 3.791A pdb=" N MET E 936 " --> pdb=" O VAL E 929 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'E' and resid 967 through 969 Processing sheet with id= AT, first strand: chain 'E' and resid 1009 through 1011 Processing sheet with id= AU, first strand: chain 'E' and resid 1079 through 1081 Processing sheet with id= AV, first strand: chain 'E' and resid 1090 through 1093 removed outlier: 3.517A pdb=" N SER E1090 " --> pdb=" O SER E1104 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'E' and resid 1132 through 1135 Processing sheet with id= AX, first strand: chain 'E' and resid 1182 through 1185 removed outlier: 4.002A pdb=" N ASP E1182 " --> pdb=" O ALA E1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA E1195 " --> pdb=" O ASP E1182 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'E' and resid 1233 through 1235 Processing sheet with id= AZ, first strand: chain 'E' and resid 660 through 665 removed outlier: 6.643A pdb=" N CYS E 675 " --> pdb=" O LEU E 661 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N CYS E 663 " --> pdb=" O ALA E 673 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA E 673 " --> pdb=" O CYS E 663 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'E' and resid 681 through 684 Processing sheet with id= BB, first strand: chain 'E' and resid 885 through 890 removed outlier: 6.368A pdb=" N SER E 900 " --> pdb=" O HIS E 886 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL E 888 " --> pdb=" O LEU E 898 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU E 898 " --> pdb=" O VAL E 888 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'G' and resid 277 through 281 removed outlier: 6.770A pdb=" N TRP G 149 " --> pdb=" O TYR G 278 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL G 280 " --> pdb=" O TRP G 149 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR G 151 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE G 260 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N ILE G 152 " --> pdb=" O ILE G 260 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU G 262 " --> pdb=" O ILE G 152 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU G 240 " --> pdb=" O LEU G 261 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR G 263 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU G 242 " --> pdb=" O THR G 263 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'G' and resid 609 through 611 removed outlier: 3.901A pdb=" N LEU G 609 " --> pdb=" O LEU G 908 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'G' and resid 621 through 623 removed outlier: 6.330A pdb=" N LYS G 643 " --> pdb=" O LYS G 649 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LYS G 649 " --> pdb=" O LYS G 643 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'G' and resid 702 through 707 removed outlier: 6.216A pdb=" N GLY G 719 " --> pdb=" O ASN G 703 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N CYS G 705 " --> pdb=" O ALA G 717 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA G 717 " --> pdb=" O CYS G 705 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE G 707 " --> pdb=" O LEU G 715 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU G 715 " --> pdb=" O PHE G 707 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP G 729 " --> pdb=" O CYS G 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS G 735 " --> pdb=" O ASP G 729 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'G' and resid 768 through 771 removed outlier: 3.846A pdb=" N HIS G 748 " --> pdb=" O CYS G 761 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'G' and resid 804 through 806 removed outlier: 5.462A pdb=" N ASP G 825 " --> pdb=" O LEU G 831 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU G 831 " --> pdb=" O ASP G 825 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'G' and resid 854 through 858 removed outlier: 5.505A pdb=" N ASN G 868 " --> pdb=" O LYS G 874 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LYS G 874 " --> pdb=" O ASN G 868 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'G' and resid 928 through 930 removed outlier: 3.791A pdb=" N MET G 936 " --> pdb=" O VAL G 929 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'G' and resid 967 through 969 Processing sheet with id= BL, first strand: chain 'G' and resid 1009 through 1011 Processing sheet with id= BM, first strand: chain 'G' and resid 1079 through 1081 Processing sheet with id= BN, first strand: chain 'G' and resid 1090 through 1093 removed outlier: 3.517A pdb=" N SER G1090 " --> pdb=" O SER G1104 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'G' and resid 1132 through 1135 Processing sheet with id= BP, first strand: chain 'G' and resid 1182 through 1185 removed outlier: 4.002A pdb=" N ASP G1182 " --> pdb=" O ALA G1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G1195 " --> pdb=" O ASP G1182 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'G' and resid 1233 through 1235 Processing sheet with id= BR, first strand: chain 'G' and resid 660 through 665 removed outlier: 6.641A pdb=" N CYS G 675 " --> pdb=" O LEU G 661 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS G 663 " --> pdb=" O ALA G 673 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA G 673 " --> pdb=" O CYS G 663 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'G' and resid 681 through 684 Processing sheet with id= BT, first strand: chain 'G' and resid 885 through 890 removed outlier: 6.368A pdb=" N SER G 900 " --> pdb=" O HIS G 886 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL G 888 " --> pdb=" O LEU G 898 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU G 898 " --> pdb=" O VAL G 888 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'I' and resid 277 through 281 removed outlier: 6.770A pdb=" N TRP I 149 " --> pdb=" O TYR I 278 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL I 280 " --> pdb=" O TRP I 149 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR I 151 " --> pdb=" O VAL I 280 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE I 260 " --> pdb=" O VAL I 150 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N ILE I 152 " --> pdb=" O ILE I 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU I 262 " --> pdb=" O ILE I 152 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU I 240 " --> pdb=" O LEU I 261 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR I 263 " --> pdb=" O LEU I 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU I 242 " --> pdb=" O THR I 263 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'I' and resid 609 through 611 removed outlier: 3.901A pdb=" N LEU I 609 " --> pdb=" O LEU I 908 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'I' and resid 621 through 623 removed outlier: 6.327A pdb=" N LYS I 643 " --> pdb=" O LYS I 649 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS I 649 " --> pdb=" O LYS I 643 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'I' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY I 719 " --> pdb=" O ASN I 703 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS I 705 " --> pdb=" O ALA I 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA I 717 " --> pdb=" O CYS I 705 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE I 707 " --> pdb=" O LEU I 715 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU I 715 " --> pdb=" O PHE I 707 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP I 729 " --> pdb=" O CYS I 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS I 735 " --> pdb=" O ASP I 729 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'I' and resid 768 through 771 removed outlier: 3.847A pdb=" N HIS I 748 " --> pdb=" O CYS I 761 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'I' and resid 804 through 806 removed outlier: 5.462A pdb=" N ASP I 825 " --> pdb=" O LEU I 831 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU I 831 " --> pdb=" O ASP I 825 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'I' and resid 854 through 858 removed outlier: 5.505A pdb=" N ASN I 868 " --> pdb=" O LYS I 874 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS I 874 " --> pdb=" O ASN I 868 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'I' and resid 928 through 930 removed outlier: 3.790A pdb=" N MET I 936 " --> pdb=" O VAL I 929 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'I' and resid 967 through 969 Processing sheet with id= CD, first strand: chain 'I' and resid 1009 through 1011 Processing sheet with id= CE, first strand: chain 'I' and resid 1079 through 1081 Processing sheet with id= CF, first strand: chain 'I' and resid 1090 through 1093 removed outlier: 3.515A pdb=" N SER I1090 " --> pdb=" O SER I1104 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'I' and resid 1132 through 1135 Processing sheet with id= CH, first strand: chain 'I' and resid 1182 through 1185 removed outlier: 4.001A pdb=" N ASP I1182 " --> pdb=" O ALA I1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA I1195 " --> pdb=" O ASP I1182 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'I' and resid 1233 through 1235 Processing sheet with id= CJ, first strand: chain 'I' and resid 660 through 665 removed outlier: 6.643A pdb=" N CYS I 675 " --> pdb=" O LEU I 661 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N CYS I 663 " --> pdb=" O ALA I 673 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA I 673 " --> pdb=" O CYS I 663 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'I' and resid 681 through 684 Processing sheet with id= CL, first strand: chain 'I' and resid 885 through 890 removed outlier: 6.367A pdb=" N SER I 900 " --> pdb=" O HIS I 886 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL I 888 " --> pdb=" O LEU I 898 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU I 898 " --> pdb=" O VAL I 888 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'K' and resid 277 through 281 removed outlier: 6.769A pdb=" N TRP K 149 " --> pdb=" O TYR K 278 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL K 280 " --> pdb=" O TRP K 149 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR K 151 " --> pdb=" O VAL K 280 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE K 260 " --> pdb=" O VAL K 150 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ILE K 152 " --> pdb=" O ILE K 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU K 262 " --> pdb=" O ILE K 152 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU K 240 " --> pdb=" O LEU K 261 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR K 263 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU K 242 " --> pdb=" O THR K 263 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'K' and resid 609 through 611 removed outlier: 3.902A pdb=" N LEU K 609 " --> pdb=" O LEU K 908 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'K' and resid 621 through 623 removed outlier: 6.328A pdb=" N LYS K 643 " --> pdb=" O LYS K 649 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS K 649 " --> pdb=" O LYS K 643 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'K' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY K 719 " --> pdb=" O ASN K 703 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N CYS K 705 " --> pdb=" O ALA K 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA K 717 " --> pdb=" O CYS K 705 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE K 707 " --> pdb=" O LEU K 715 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU K 715 " --> pdb=" O PHE K 707 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP K 729 " --> pdb=" O CYS K 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS K 735 " --> pdb=" O ASP K 729 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'K' and resid 768 through 771 removed outlier: 3.846A pdb=" N HIS K 748 " --> pdb=" O CYS K 761 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'K' and resid 804 through 806 removed outlier: 5.463A pdb=" N ASP K 825 " --> pdb=" O LEU K 831 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU K 831 " --> pdb=" O ASP K 825 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'K' and resid 854 through 858 removed outlier: 5.504A pdb=" N ASN K 868 " --> pdb=" O LYS K 874 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS K 874 " --> pdb=" O ASN K 868 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'K' and resid 928 through 930 removed outlier: 3.792A pdb=" N MET K 936 " --> pdb=" O VAL K 929 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'K' and resid 967 through 969 Processing sheet with id= CV, first strand: chain 'K' and resid 1009 through 1011 Processing sheet with id= CW, first strand: chain 'K' and resid 1079 through 1081 Processing sheet with id= CX, first strand: chain 'K' and resid 1090 through 1093 removed outlier: 3.517A pdb=" N SER K1090 " --> pdb=" O SER K1104 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'K' and resid 1132 through 1135 Processing sheet with id= CZ, first strand: chain 'K' and resid 1182 through 1185 removed outlier: 4.002A pdb=" N ASP K1182 " --> pdb=" O ALA K1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA K1195 " --> pdb=" O ASP K1182 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'K' and resid 1233 through 1235 Processing sheet with id= DB, first strand: chain 'K' and resid 660 through 665 removed outlier: 6.641A pdb=" N CYS K 675 " --> pdb=" O LEU K 661 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N CYS K 663 " --> pdb=" O ALA K 673 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA K 673 " --> pdb=" O CYS K 663 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'K' and resid 681 through 684 Processing sheet with id= DD, first strand: chain 'K' and resid 885 through 890 removed outlier: 6.367A pdb=" N SER K 900 " --> pdb=" O HIS K 886 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL K 888 " --> pdb=" O LEU K 898 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU K 898 " --> pdb=" O VAL K 888 " (cutoff:3.500A) Processing sheet with id= DE, first strand: chain 'M' and resid 277 through 281 removed outlier: 6.770A pdb=" N TRP M 149 " --> pdb=" O TYR M 278 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL M 280 " --> pdb=" O TRP M 149 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR M 151 " --> pdb=" O VAL M 280 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE M 260 " --> pdb=" O VAL M 150 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ILE M 152 " --> pdb=" O ILE M 260 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU M 262 " --> pdb=" O ILE M 152 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU M 240 " --> pdb=" O LEU M 261 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR M 263 " --> pdb=" O LEU M 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU M 242 " --> pdb=" O THR M 263 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain 'M' and resid 609 through 611 removed outlier: 3.902A pdb=" N LEU M 609 " --> pdb=" O LEU M 908 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'M' and resid 621 through 623 removed outlier: 6.329A pdb=" N LYS M 643 " --> pdb=" O LYS M 649 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LYS M 649 " --> pdb=" O LYS M 643 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain 'M' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY M 719 " --> pdb=" O ASN M 703 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS M 705 " --> pdb=" O ALA M 717 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ALA M 717 " --> pdb=" O CYS M 705 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE M 707 " --> pdb=" O LEU M 715 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU M 715 " --> pdb=" O PHE M 707 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP M 729 " --> pdb=" O CYS M 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS M 735 " --> pdb=" O ASP M 729 " (cutoff:3.500A) Processing sheet with id= DI, first strand: chain 'M' and resid 768 through 771 removed outlier: 3.844A pdb=" N HIS M 748 " --> pdb=" O CYS M 761 " (cutoff:3.500A) Processing sheet with id= DJ, first strand: chain 'M' and resid 804 through 806 removed outlier: 5.462A pdb=" N ASP M 825 " --> pdb=" O LEU M 831 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU M 831 " --> pdb=" O ASP M 825 " (cutoff:3.500A) Processing sheet with id= DK, first strand: chain 'M' and resid 854 through 858 removed outlier: 5.505A pdb=" N ASN M 868 " --> pdb=" O LYS M 874 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS M 874 " --> pdb=" O ASN M 868 " (cutoff:3.500A) Processing sheet with id= DL, first strand: chain 'M' and resid 928 through 930 removed outlier: 3.790A pdb=" N MET M 936 " --> pdb=" O VAL M 929 " (cutoff:3.500A) Processing sheet with id= DM, first strand: chain 'M' and resid 967 through 969 Processing sheet with id= DN, first strand: chain 'M' and resid 1009 through 1011 Processing sheet with id= DO, first strand: chain 'M' and resid 1079 through 1081 Processing sheet with id= DP, first strand: chain 'M' and resid 1090 through 1093 removed outlier: 3.516A pdb=" N SER M1090 " --> pdb=" O SER M1104 " (cutoff:3.500A) Processing sheet with id= DQ, first strand: chain 'M' and resid 1132 through 1135 Processing sheet with id= DR, first strand: chain 'M' and resid 1182 through 1185 removed outlier: 4.001A pdb=" N ASP M1182 " --> pdb=" O ALA M1195 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA M1195 " --> pdb=" O ASP M1182 " (cutoff:3.500A) Processing sheet with id= DS, first strand: chain 'M' and resid 1233 through 1235 Processing sheet with id= DT, first strand: chain 'M' and resid 660 through 665 removed outlier: 6.642A pdb=" N CYS M 675 " --> pdb=" O LEU M 661 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N CYS M 663 " --> pdb=" O ALA M 673 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA M 673 " --> pdb=" O CYS M 663 " (cutoff:3.500A) Processing sheet with id= DU, first strand: chain 'M' and resid 681 through 684 Processing sheet with id= DV, first strand: chain 'M' and resid 885 through 890 removed outlier: 6.366A pdb=" N SER M 900 " --> pdb=" O HIS M 886 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL M 888 " --> pdb=" O LEU M 898 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU M 898 " --> pdb=" O VAL M 888 " (cutoff:3.500A) 2326 hydrogen bonds defined for protein. 6348 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: 34.29 Time building geometry restraints manager: 26.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 26796 1.37 - 1.55: 52476 1.55 - 1.73: 235 1.73 - 1.92: 728 1.92 - 2.10: 21 Bond restraints: 80256 Sorted by residual: bond pdb=" C TRP K1179 " pdb=" N VAL K1180 " ideal model delta sigma weight residual 1.332 1.190 0.142 1.36e-02 5.41e+03 1.09e+02 bond pdb=" C4 DTP E1301 " pdb=" C5 DTP E1301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.94e+01 bond pdb=" C4 DTP A1301 " pdb=" C5 DTP A1301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.87e+01 bond pdb=" C4 DTP G1301 " pdb=" C5 DTP G1301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C4 DTP I1301 " pdb=" C5 DTP I1301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.84e+01 ... (remaining 80251 not shown) Histogram of bond angle deviations from ideal: 85.94 - 104.38: 990 104.38 - 122.82: 97071 122.82 - 141.26: 10468 141.26 - 159.70: 0 159.70 - 178.14: 14 Bond angle restraints: 108543 Sorted by residual: angle pdb=" PB DTP E1301 " pdb=" O3B DTP E1301 " pdb=" PG DTP E1301 " ideal model delta sigma weight residual 139.87 120.39 19.48 1.00e+00 1.00e+00 3.80e+02 angle pdb=" PB DTP A1301 " pdb=" O3B DTP A1301 " pdb=" PG DTP A1301 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB DTP I1301 " pdb=" O3B DTP I1301 " pdb=" PG DTP I1301 " ideal model delta sigma weight residual 139.87 120.49 19.38 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB DTP C1301 " pdb=" O3B DTP C1301 " pdb=" PG DTP C1301 " ideal model delta sigma weight residual 139.87 120.52 19.35 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB DTP M1301 " pdb=" O3B DTP M1301 " pdb=" PG DTP M1301 " ideal model delta sigma weight residual 139.87 120.53 19.34 1.00e+00 1.00e+00 3.74e+02 ... (remaining 108538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.25: 43815 26.25 - 52.49: 3430 52.49 - 78.74: 942 78.74 - 104.98: 124 104.98 - 131.23: 7 Dihedral angle restraints: 48318 sinusoidal: 19896 harmonic: 28422 Sorted by residual: dihedral pdb=" CB CYS M 761 " pdb=" SG CYS M 761 " pdb=" SG CYS M 804 " pdb=" CB CYS M 804 " ideal model delta sinusoidal sigma weight residual 93.00 174.18 -81.18 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CB CYS A 761 " pdb=" SG CYS A 761 " pdb=" SG CYS A 804 " pdb=" CB CYS A 804 " ideal model delta sinusoidal sigma weight residual 93.00 174.14 -81.14 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS E 761 " pdb=" SG CYS E 761 " pdb=" SG CYS E 804 " pdb=" CB CYS E 804 " ideal model delta sinusoidal sigma weight residual 93.00 174.13 -81.13 1 1.00e+01 1.00e-02 8.12e+01 ... (remaining 48315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 9998 0.096 - 0.192: 1594 0.192 - 0.288: 338 0.288 - 0.383: 49 0.383 - 0.479: 14 Chirality restraints: 11993 Sorted by residual: chirality pdb=" CA HIS A 153 " pdb=" N HIS A 153 " pdb=" C HIS A 153 " pdb=" CB HIS A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CA HIS E 153 " pdb=" N HIS E 153 " pdb=" C HIS E 153 " pdb=" CB HIS E 153 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CA HIS G 153 " pdb=" N HIS G 153 " pdb=" C HIS G 153 " pdb=" CB HIS G 153 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.73e+00 ... (remaining 11990 not shown) Planarity restraints: 13790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG T 52 " -0.677 9.50e-02 1.11e+02 3.04e-01 5.62e+01 pdb=" NE ARG T 52 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG T 52 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG T 52 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG T 52 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE M 560 " -0.102 5.00e-02 4.00e+02 1.60e-01 4.09e+01 pdb=" N PRO M 561 " 0.277 5.00e-02 4.00e+02 pdb=" CA PRO M 561 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO M 561 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 560 " 0.102 5.00e-02 4.00e+02 1.60e-01 4.08e+01 pdb=" N PRO C 561 " -0.276 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " 0.079 5.00e-02 4.00e+02 ... (remaining 13787 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 245 2.17 - 2.86: 31574 2.86 - 3.54: 114044 3.54 - 4.22: 189357 4.22 - 4.90: 312739 Nonbonded interactions: 647959 Sorted by model distance: nonbonded pdb=" OG SER A 141 " pdb=" CD1 LEU W 10 " model vdw 1.493 3.460 nonbonded pdb=" O TRP E 483 " pdb=" CB LEU E 487 " model vdw 1.816 3.440 nonbonded pdb=" O TRP C 483 " pdb=" CB LEU C 487 " model vdw 1.816 3.440 nonbonded pdb=" O TRP G 483 " pdb=" CB LEU G 487 " model vdw 1.816 3.440 nonbonded pdb=" O TRP A 483 " pdb=" CB LEU A 487 " model vdw 1.816 3.440 ... (remaining 647954 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' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = (chain 'W' and resid 1 through 91) selection = (chain 'X' and resid 1 through 91) } ncs_group { reference = (chain 'S' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 95)) selection = (chain 'T' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 95)) selection = (chain 'U' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 95)) selection = (chain 'V' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 95)) selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 11.730 Check model and map are aligned: 0.890 Set scattering table: 0.530 Process input model: 165.620 Find NCS groups from input model: 4.430 Set up NCS constraints: 0.750 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 188.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1510 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 : 0.008 0.217 80256 Z= 0.537 Angle : 1.345 19.482 108543 Z= 0.941 Chirality : 0.076 0.479 11993 Planarity : 0.010 0.304 13790 Dihedral : 19.501 131.230 29773 Min Nonbonded Distance : 1.493 Molprobity Statistics. All-atom Clashscore : 69.05 Ramachandran Plot: Outliers : 3.39 % Allowed : 7.12 % Favored : 89.49 % Rotamer: Outliers : 16.86 % Allowed : 10.68 % Favored : 72.46 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.09), residues: 9716 helix: 0.00 (0.09), residues: 3194 sheet: -1.64 (0.16), residues: 1148 loop : -0.43 (0.09), residues: 5374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 249 HIS 0.014 0.001 HIS L 33 PHE 0.055 0.002 PHE R 34 TYR 0.044 0.004 TYR P 72 ARG 0.024 0.001 ARG S 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2773 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1467 poor density : 1306 time to evaluate : 6.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 HIS cc_start: 0.4058 (p-80) cc_final: 0.3718 (p90) REVERT: A 261 LEU cc_start: 0.2615 (OUTLIER) cc_final: 0.1839 (tt) REVERT: A 273 VAL cc_start: 0.5594 (OUTLIER) cc_final: 0.5344 (p) REVERT: A 352 ARG cc_start: 0.5408 (OUTLIER) cc_final: 0.4884 (mmp-170) REVERT: A 568 LEU cc_start: -0.3074 (OUTLIER) cc_final: -0.4189 (tt) REVERT: A 588 VAL cc_start: 0.3416 (OUTLIER) cc_final: 0.3102 (t) REVERT: A 600 LYS cc_start: 0.0813 (OUTLIER) cc_final: -0.1111 (ptpt) REVERT: A 643 LYS cc_start: 0.0102 (OUTLIER) cc_final: -0.0329 (tmtt) REVERT: A 739 MET cc_start: -0.3745 (mtm) cc_final: -0.3970 (mtt) REVERT: A 885 VAL cc_start: -0.0107 (OUTLIER) cc_final: -0.0674 (p) REVERT: A 914 VAL cc_start: 0.0004 (OUTLIER) cc_final: -0.0427 (m) REVERT: A 925 GLU cc_start: -0.0820 (OUTLIER) cc_final: -0.2253 (tt0) REVERT: A 936 MET cc_start: 0.1877 (mtp) cc_final: 0.1179 (ptm) REVERT: A 1191 MET cc_start: -0.2525 (mtm) cc_final: -0.3831 (tmm) REVERT: A 1235 VAL cc_start: 0.3773 (OUTLIER) cc_final: 0.3194 (p) REVERT: A 1243 ILE cc_start: 0.5813 (mt) cc_final: 0.5382 (mt) REVERT: C 174 LEU cc_start: 0.2170 (OUTLIER) cc_final: 0.0788 (tp) REVERT: C 252 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.7012 (mmmm) REVERT: C 273 VAL cc_start: 0.0822 (OUTLIER) cc_final: 0.0591 (p) REVERT: C 442 VAL cc_start: 0.3946 (OUTLIER) cc_final: 0.3658 (p) REVERT: C 473 LEU cc_start: -0.2829 (OUTLIER) cc_final: -0.3616 (mt) REVERT: C 550 LEU cc_start: -0.2377 (OUTLIER) cc_final: -0.2766 (pp) REVERT: C 588 VAL cc_start: -0.3523 (OUTLIER) cc_final: -0.3802 (t) REVERT: C 651 LEU cc_start: -0.2294 (OUTLIER) cc_final: -0.3722 (mt) REVERT: C 879 ARG cc_start: 0.0027 (OUTLIER) cc_final: -0.2100 (mmm160) REVERT: C 1168 LEU cc_start: 0.1759 (OUTLIER) cc_final: 0.1073 (mt) REVERT: C 1181 THR cc_start: 0.1591 (OUTLIER) cc_final: 0.1178 (p) REVERT: E 149 TRP cc_start: 0.1019 (m-10) cc_final: 0.0432 (m-10) REVERT: E 213 SER cc_start: 0.6620 (OUTLIER) cc_final: 0.6332 (t) REVERT: E 261 LEU cc_start: -0.2869 (OUTLIER) cc_final: -0.3875 (tt) REVERT: E 268 SER cc_start: 0.6077 (OUTLIER) cc_final: 0.5815 (m) REVERT: E 473 LEU cc_start: -0.3704 (OUTLIER) cc_final: -0.5830 (mp) REVERT: E 588 VAL cc_start: -0.1763 (OUTLIER) cc_final: -0.2456 (p) REVERT: E 646 THR cc_start: -0.3352 (OUTLIER) cc_final: -0.3684 (t) REVERT: E 879 ARG cc_start: 0.1266 (OUTLIER) cc_final: 0.0326 (mmm160) REVERT: E 999 ARG cc_start: 0.2514 (OUTLIER) cc_final: 0.0546 (tpt90) REVERT: E 1183 LEU cc_start: -0.1038 (OUTLIER) cc_final: -0.1542 (mt) REVERT: F 50 ASP cc_start: 0.3522 (m-30) cc_final: 0.3211 (m-30) REVERT: G 202 LEU cc_start: 0.6996 (tp) cc_final: 0.6451 (tp) REVERT: G 325 SER cc_start: -0.0442 (OUTLIER) cc_final: -0.0842 (p) REVERT: G 473 LEU cc_start: -0.3589 (OUTLIER) cc_final: -0.5135 (mp) REVERT: G 504 MET cc_start: -0.2539 (mtp) cc_final: -0.2801 (mtm) REVERT: G 530 ARG cc_start: 0.0005 (OUTLIER) cc_final: -0.0308 (ttp-170) REVERT: G 531 HIS cc_start: -0.3750 (OUTLIER) cc_final: -0.4190 (t-170) REVERT: G 603 ILE cc_start: 0.0213 (OUTLIER) cc_final: -0.0213 (pt) REVERT: G 651 LEU cc_start: -0.1891 (OUTLIER) cc_final: -0.2724 (mt) REVERT: G 1171 GLU cc_start: 0.1450 (OUTLIER) cc_final: 0.0727 (pt0) REVERT: G 1183 LEU cc_start: -0.1660 (OUTLIER) cc_final: -0.2194 (mp) REVERT: I 127 VAL cc_start: 0.5298 (OUTLIER) cc_final: 0.5003 (p) REVERT: I 160 LYS cc_start: 0.0918 (OUTLIER) cc_final: 0.0541 (mttt) REVERT: I 230 LEU cc_start: 0.7255 (mt) cc_final: 0.6808 (mp) REVERT: I 450 CYS cc_start: 0.2802 (OUTLIER) cc_final: 0.2403 (t) REVERT: I 522 LEU cc_start: -0.2893 (OUTLIER) cc_final: -0.3151 (mp) REVERT: I 530 ARG cc_start: 0.1016 (OUTLIER) cc_final: -0.0968 (ttm170) REVERT: I 531 HIS cc_start: -0.3847 (OUTLIER) cc_final: -0.6213 (t70) REVERT: I 553 HIS cc_start: 0.0672 (OUTLIER) cc_final: -0.0600 (t70) REVERT: I 568 LEU cc_start: -0.1417 (OUTLIER) cc_final: -0.2747 (tp) REVERT: I 651 LEU cc_start: -0.1725 (OUTLIER) cc_final: -0.2108 (mt) REVERT: I 687 MET cc_start: -0.1868 (ttp) cc_final: -0.3677 (ptp) REVERT: I 802 LYS cc_start: -0.0490 (mmtt) cc_final: -0.2092 (mptt) REVERT: I 925 GLU cc_start: -0.2133 (OUTLIER) cc_final: -0.2763 (pt0) REVERT: I 936 MET cc_start: -0.1284 (mtp) cc_final: -0.2533 (ttt) REVERT: I 1221 LYS cc_start: -0.0754 (OUTLIER) cc_final: -0.2921 (tptt) REVERT: I 1235 VAL cc_start: 0.5467 (OUTLIER) cc_final: 0.4158 (p) REVERT: I 1247 LEU cc_start: 0.1586 (OUTLIER) cc_final: 0.1100 (mp) REVERT: I 1248 GLU cc_start: 0.3056 (OUTLIER) cc_final: 0.2755 (pt0) REVERT: K 160 LYS cc_start: 0.2950 (OUTLIER) cc_final: 0.2693 (tttt) REVERT: K 202 LEU cc_start: 0.7487 (tp) cc_final: 0.7176 (tp) REVERT: K 239 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6440 (tp) REVERT: K 290 LYS cc_start: 0.1472 (OUTLIER) cc_final: 0.0640 (mtmt) REVERT: K 374 MET cc_start: -0.0316 (OUTLIER) cc_final: -0.0651 (ptt) REVERT: K 397 THR cc_start: -0.3593 (OUTLIER) cc_final: -0.3850 (p) REVERT: K 449 ASN cc_start: -0.1269 (OUTLIER) cc_final: -0.2718 (t0) REVERT: K 473 LEU cc_start: -0.3110 (OUTLIER) cc_final: -0.4109 (mp) REVERT: K 522 LEU cc_start: 0.4326 (OUTLIER) cc_final: 0.2365 (mp) REVERT: K 533 LEU cc_start: -0.5701 (OUTLIER) cc_final: -0.5963 (mp) REVERT: K 572 GLU cc_start: -0.1864 (OUTLIER) cc_final: -0.3046 (tm-30) REVERT: K 633 CYS cc_start: 0.1406 (OUTLIER) cc_final: 0.0104 (m) REVERT: K 643 LYS cc_start: -0.1152 (OUTLIER) cc_final: -0.2411 (tttp) REVERT: K 739 MET cc_start: -0.2290 (mtm) cc_final: -0.2742 (mtm) REVERT: K 925 GLU cc_start: -0.0701 (OUTLIER) cc_final: -0.3669 (tm-30) REVERT: K 926 VAL cc_start: 0.4053 (m) cc_final: 0.3086 (m) REVERT: K 936 MET cc_start: -0.2290 (mtp) cc_final: -0.3096 (ttt) REVERT: K 948 LEU cc_start: -0.2313 (OUTLIER) cc_final: -0.2762 (mt) REVERT: K 1078 GLU cc_start: 0.4150 (OUTLIER) cc_final: 0.2757 (pt0) REVERT: K 1171 GLU cc_start: 0.1724 (OUTLIER) cc_final: 0.0879 (mm-30) REVERT: K 1192 LEU cc_start: 0.2942 (OUTLIER) cc_final: 0.2412 (tt) REVERT: M 206 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6089 (tp) REVERT: M 283 GLU cc_start: 0.3702 (OUTLIER) cc_final: 0.3145 (mp0) REVERT: M 405 ASP cc_start: 0.4106 (OUTLIER) cc_final: 0.3628 (t0) REVERT: M 449 ASN cc_start: 0.2496 (OUTLIER) cc_final: 0.1745 (t0) REVERT: M 600 LYS cc_start: 0.3555 (OUTLIER) cc_final: 0.1672 (pttm) REVERT: M 619 TYR cc_start: -0.1169 (OUTLIER) cc_final: -0.1765 (m-80) REVERT: M 633 CYS cc_start: 0.1318 (OUTLIER) cc_final: 0.0715 (m) REVERT: M 643 LYS cc_start: -0.0459 (OUTLIER) cc_final: -0.1465 (tttt) REVERT: M 648 GLU cc_start: -0.2376 (OUTLIER) cc_final: -0.3540 (pm20) REVERT: M 659 GLU cc_start: -0.0958 (OUTLIER) cc_final: -0.2248 (mt-10) REVERT: M 739 MET cc_start: -0.2175 (mtm) cc_final: -0.2680 (mtm) REVERT: M 948 LEU cc_start: -0.3994 (OUTLIER) cc_final: -0.4467 (mp) REVERT: M 1165 CYS cc_start: -0.4199 (OUTLIER) cc_final: -0.5450 (t) REVERT: M 1215 THR cc_start: 0.3233 (OUTLIER) cc_final: 0.2919 (t) REVERT: M 1248 GLU cc_start: 0.4223 (OUTLIER) cc_final: 0.3342 (pm20) REVERT: Q 42 LYS cc_start: 0.6956 (mttp) cc_final: 0.6671 (tptp) REVERT: S 36 ARG cc_start: -0.1928 (OUTLIER) cc_final: -0.2285 (mmt-90) REVERT: T 1 MET cc_start: -0.3534 (ttm) cc_final: -0.5268 (tpp) REVERT: T 8 LEU cc_start: -0.0716 (OUTLIER) cc_final: -0.1151 (tp) REVERT: U 1 MET cc_start: -0.1396 (ttm) cc_final: -0.1627 (ttm) REVERT: W 26 MET cc_start: -0.1074 (mtm) cc_final: -0.1276 (mtt) outliers start: 1467 outliers final: 255 residues processed: 2444 average time/residue: 0.7770 time to fit residues: 3142.7806 Evaluate side-chains 1192 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 851 time to evaluate : 6.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 816 optimal weight: 7.9990 chunk 732 optimal weight: 20.0000 chunk 406 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 494 optimal weight: 8.9990 chunk 391 optimal weight: 6.9990 chunk 757 optimal weight: 0.5980 chunk 293 optimal weight: 2.9990 chunk 460 optimal weight: 9.9990 chunk 564 optimal weight: 0.0170 chunk 878 optimal weight: 3.9990 overall best weight: 1.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 347 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A1163 HIS ** A1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS B 52 ASN C 235 HIS C 420 ASN C 463 GLN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 GLN ** C 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN ** C 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 GLN C 640 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 933 ASN ** C1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN E 134 ASN E 183 HIS ** E 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 ASN E 429 ASN ** E 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN E 463 GLN E 477 GLN E 545 GLN ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 565 GLN E 583 GLN E 599 ASN ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 ASN ** E 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 933 ASN ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN G 183 HIS G 235 HIS ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 347 ASN ** G 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 553 HIS ** G 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 881 HIS ** G 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 933 ASN ** G1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 201 ASN I 235 HIS I 347 ASN I 429 ASN I 438 HIS I 463 GLN I 477 GLN I 553 HIS ** I 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 583 GLN ** I 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 709 ASN I 737 ASN ** I 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 933 ASN ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1219 ASN ** I1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 HIS K 153 HIS ** K 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 201 ASN ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 311 HIS K 347 ASN ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 463 GLN K 477 GLN K 545 GLN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 583 GLN ** K 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 709 ASN K 840 HIS ** K 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 933 ASN K1001 GLN ** K1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 HIS L 52 ASN M 183 HIS ** M 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 347 ASN M 429 ASN M 452 GLN M 454 GLN M 463 GLN M 477 GLN M 553 HIS ** M 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 562 ASN M 578 GLN M 583 GLN ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 709 ASN ** M 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 933 ASN M 942 HIS ** M 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 33 HIS O 28 HIS O 45 ASN O 65 ASN P 28 HIS P 45 ASN P 51 GLN P 65 ASN ** P 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 45 ASN Q 51 GLN Q 65 ASN Q 88 HIS R 11 GLN R 28 HIS R 45 ASN R 65 ASN S 24 GLN S 38 HIS S 44 GLN S 82 GLN ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 44 GLN T 82 GLN U 21 GLN U 82 GLN V 44 GLN V 82 GLN W 7 ASN W 11 GLN W 45 ASN W 51 GLN X 7 ASN X 11 GLN X 51 GLN Y 44 GLN Total number of N/Q/H flips: 114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1850 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 80256 Z= 0.265 Angle : 0.838 14.607 108543 Z= 0.431 Chirality : 0.048 0.288 11993 Planarity : 0.006 0.114 13790 Dihedral : 8.499 125.467 10669 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.36 % Favored : 92.87 % Rotamer: Outliers : 0.23 % Allowed : 3.52 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.23 (0.08), residues: 9716 helix: 0.00 (0.08), residues: 3189 sheet: -1.60 (0.13), residues: 1505 loop : -1.04 (0.09), residues: 5022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP I 404 HIS 0.016 0.002 HIS T 38 PHE 0.032 0.002 PHE G 298 TYR 0.034 0.003 TYR N 74 ARG 0.021 0.001 ARG D 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1004 time to evaluate : 6.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLN cc_start: 0.6277 (pp30) cc_final: 0.5981 (pp30) REVERT: A 255 ASP cc_start: 0.6264 (t0) cc_final: 0.5803 (t0) REVERT: A 353 ILE cc_start: 0.5698 (mt) cc_final: 0.5257 (mt) REVERT: A 378 ASP cc_start: 0.5424 (OUTLIER) cc_final: 0.4660 (p0) REVERT: A 701 GLN cc_start: 0.2058 (pm20) cc_final: 0.1697 (pm20) REVERT: A 739 MET cc_start: -0.3671 (mtm) cc_final: -0.4872 (mtt) REVERT: C 359 TYR cc_start: 0.5191 (t80) cc_final: 0.4918 (t80) REVERT: C 540 VAL cc_start: 0.5314 (t) cc_final: 0.5096 (t) REVERT: C 592 MET cc_start: -0.3292 (mtp) cc_final: -0.4538 (ttm) REVERT: C 640 GLN cc_start: 0.0870 (OUTLIER) cc_final: 0.0607 (pp30) REVERT: C 687 MET cc_start: -0.0644 (pmm) cc_final: -0.1122 (pmm) REVERT: E 252 LYS cc_start: 0.7209 (mmmt) cc_final: 0.6989 (mmmm) REVERT: E 481 MET cc_start: -0.1129 (ppp) cc_final: -0.1381 (ppp) REVERT: E 840 HIS cc_start: 0.4295 (m90) cc_final: 0.3790 (m-70) REVERT: G 504 MET cc_start: -0.2415 (mtp) cc_final: -0.2952 (mtp) REVERT: G 592 MET cc_start: -0.3217 (mtm) cc_final: -0.3811 (ptp) REVERT: I 206 LEU cc_start: 0.7847 (tp) cc_final: 0.7395 (tt) REVERT: I 406 MET cc_start: -0.1346 (tmm) cc_final: -0.1917 (ptm) REVERT: I 687 MET cc_start: -0.0882 (ttp) cc_final: -0.2526 (ptp) REVERT: I 802 LYS cc_start: -0.0382 (mmtt) cc_final: -0.2257 (mptt) REVERT: K 358 SER cc_start: 0.5472 (m) cc_final: 0.5268 (p) REVERT: K 368 MET cc_start: 0.4520 (mmt) cc_final: 0.3819 (mtm) REVERT: K 739 MET cc_start: -0.2367 (mtm) cc_final: -0.2780 (mtm) REVERT: K 936 MET cc_start: -0.2336 (mtp) cc_final: -0.3272 (ttt) REVERT: M 141 SER cc_start: 0.7098 (m) cc_final: 0.6259 (m) REVERT: M 739 MET cc_start: -0.2107 (mtm) cc_final: -0.2877 (mtm) REVERT: O 59 MET cc_start: -0.1559 (ttp) cc_final: -0.1885 (ttm) REVERT: P 26 MET cc_start: 0.6522 (mtt) cc_final: 0.6148 (mmt) REVERT: T 1 MET cc_start: -0.3379 (ttm) cc_final: -0.5264 (tpp) REVERT: U 64 THR cc_start: 0.4007 (p) cc_final: 0.3701 (p) REVERT: V 1 MET cc_start: -0.0203 (ttp) cc_final: -0.0954 (ptm) REVERT: W 55 MET cc_start: 0.0176 (ptp) cc_final: -0.2074 (ppp) outliers start: 20 outliers final: 0 residues processed: 1023 average time/residue: 0.7639 time to fit residues: 1312.8588 Evaluate side-chains 696 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 694 time to evaluate : 6.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 488 optimal weight: 50.0000 chunk 272 optimal weight: 0.4980 chunk 730 optimal weight: 30.0000 chunk 597 optimal weight: 0.0010 chunk 242 optimal weight: 30.0000 chunk 879 optimal weight: 0.0370 chunk 950 optimal weight: 3.9990 chunk 783 optimal weight: 7.9990 chunk 872 optimal weight: 0.6980 chunk 299 optimal weight: 2.9990 chunk 705 optimal weight: 5.9990 overall best weight: 0.8466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN A 531 HIS A 545 GLN ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN ** A1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS C 347 ASN C 521 HIS ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN C 565 GLN C 737 ASN C 748 HIS ** C1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 ASN ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 GLN E 420 ASN ** E 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN E 553 HIS ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 706 HIS ** E 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1237 ASN F 52 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 449 ASN G 463 GLN ** G 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1237 ASN H 12 GLN H 42 GLN I 183 HIS I 429 ASN I 452 GLN I 477 GLN I 565 GLN I 583 GLN ** I 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 942 HIS ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1237 ASN ** K 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 438 HIS ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 840 HIS ** K 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1237 ASN L 42 GLN M 235 HIS ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 429 ASN M 477 GLN M 562 ASN ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 904 GLN M1224 HIS M1237 ASN ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1901 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 80256 Z= 0.197 Angle : 0.704 9.848 108543 Z= 0.359 Chirality : 0.043 0.218 11993 Planarity : 0.004 0.071 13790 Dihedral : 8.051 110.764 10669 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.67 % Favored : 92.65 % Rotamer: Outliers : 0.07 % Allowed : 3.24 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.08), residues: 9716 helix: 0.12 (0.09), residues: 3174 sheet: -1.75 (0.12), residues: 1659 loop : -1.11 (0.09), residues: 4883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP I 404 HIS 0.016 0.001 HIS K 840 PHE 0.046 0.002 PHE C 298 TYR 0.043 0.002 TYR C 435 ARG 0.017 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 863 time to evaluate : 6.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.7165 (m110) cc_final: 0.5095 (m110) REVERT: A 255 ASP cc_start: 0.6198 (t0) cc_final: 0.5962 (t0) REVERT: A 368 MET cc_start: 0.6637 (ttm) cc_final: 0.6369 (ttm) REVERT: A 381 ASP cc_start: 0.6880 (p0) cc_final: 0.6658 (p0) REVERT: A 701 GLN cc_start: 0.2073 (pm20) cc_final: 0.1576 (pm20) REVERT: A 739 MET cc_start: -0.3708 (mtm) cc_final: -0.4608 (mtt) REVERT: C 229 ILE cc_start: 0.5715 (tt) cc_final: 0.5275 (tt) REVERT: C 322 LEU cc_start: 0.6510 (tp) cc_final: 0.6238 (tp) REVERT: C 372 VAL cc_start: 0.7477 (m) cc_final: 0.7124 (m) REVERT: C 592 MET cc_start: -0.3552 (mtp) cc_final: -0.4134 (ttm) REVERT: C 687 MET cc_start: -0.0466 (pmm) cc_final: -0.1010 (pmm) REVERT: C 889 MET cc_start: -0.2128 (tpt) cc_final: -0.3248 (mtm) REVERT: E 840 HIS cc_start: 0.4750 (m90) cc_final: 0.4153 (m-70) REVERT: G 592 MET cc_start: -0.3091 (mtm) cc_final: -0.3730 (ptp) REVERT: G 1191 MET cc_start: -0.1196 (tmm) cc_final: -0.1486 (ppp) REVERT: I 119 VAL cc_start: 0.7113 (m) cc_final: 0.6795 (m) REVERT: I 151 THR cc_start: 0.4053 (m) cc_final: 0.3775 (m) REVERT: I 687 MET cc_start: -0.0627 (ttp) cc_final: -0.2702 (ptp) REVERT: I 802 LYS cc_start: -0.0340 (mmtt) cc_final: -0.2229 (mptt) REVERT: K 155 MET cc_start: 0.1117 (ppp) cc_final: 0.0262 (ppp) REVERT: K 301 MET cc_start: 0.0765 (ptt) cc_final: 0.0115 (ptt) REVERT: K 358 SER cc_start: 0.6119 (m) cc_final: 0.5764 (p) REVERT: K 436 TYR cc_start: 0.1074 (p90) cc_final: 0.0853 (p90) REVERT: K 797 MET cc_start: -0.1095 (ttt) cc_final: -0.1608 (ttm) REVERT: K 936 MET cc_start: -0.2316 (mtp) cc_final: -0.4093 (ttt) REVERT: M 301 MET cc_start: 0.1152 (ptp) cc_final: 0.0766 (ptp) REVERT: M 374 MET cc_start: 0.4282 (mmm) cc_final: 0.3748 (mmp) REVERT: M 739 MET cc_start: -0.1750 (mtm) cc_final: -0.2603 (mtm) REVERT: M 1016 LYS cc_start: 0.3682 (mmmt) cc_final: 0.3171 (mmmt) REVERT: T 1 MET cc_start: -0.3302 (ttm) cc_final: -0.5155 (tpp) REVERT: U 1 MET cc_start: -0.0894 (ttt) cc_final: -0.1452 (ttm) REVERT: U 39 MET cc_start: 0.2110 (mmt) cc_final: 0.1784 (mmm) outliers start: 6 outliers final: 0 residues processed: 868 average time/residue: 0.7437 time to fit residues: 1103.1616 Evaluate side-chains 634 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 634 time to evaluate : 6.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 869 optimal weight: 20.0000 chunk 661 optimal weight: 2.9990 chunk 456 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 419 optimal weight: 20.0000 chunk 590 optimal weight: 30.0000 chunk 882 optimal weight: 1.9990 chunk 934 optimal weight: 0.0170 chunk 461 optimal weight: 30.0000 chunk 836 optimal weight: 40.0000 chunk 251 optimal weight: 0.0870 overall best weight: 2.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN A 420 ASN A 468 HIS A 565 GLN ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 HIS C 257 GLN C 336 ASN C 420 ASN C 441 GLN C 531 HIS C 562 ASN ** C1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN E 524 HIS E 562 ASN ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 840 HIS ** E 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN G 171 HIS ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 311 HIS ** G 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 524 HIS ** G 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 579 GLN G 706 HIS ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1176 HIS I 311 HIS ** I 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 429 ASN I 477 GLN ** I 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 904 GLN ** I1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1219 ASN K 137 GLN K 257 GLN ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 438 HIS K 449 ASN K 531 HIS ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 840 HIS K 904 GLN K1055 ASN ** K1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 390 GLN M 656 HIS M1095 HIS N 42 GLN P 45 ASN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 54 GLN X 12 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2136 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 80256 Z= 0.206 Angle : 0.695 17.410 108543 Z= 0.354 Chirality : 0.043 0.215 11993 Planarity : 0.004 0.062 13790 Dihedral : 7.970 111.087 10669 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.52 % Favored : 92.82 % Rotamer: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.57 % 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: -1.37 (0.08), residues: 9716 helix: 0.05 (0.09), residues: 3200 sheet: -1.66 (0.12), residues: 1631 loop : -1.23 (0.09), residues: 4885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 184 HIS 0.018 0.001 HIS G1084 PHE 0.044 0.002 PHE C 526 TYR 0.032 0.002 TYR G 489 ARG 0.011 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 850 time to evaluate : 6.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 160 LYS cc_start: 0.6291 (mtmt) cc_final: 0.5827 (mtmt) REVERT: A 255 ASP cc_start: 0.6468 (t0) cc_final: 0.6187 (t0) REVERT: A 687 MET cc_start: 0.1111 (mpp) cc_final: 0.0792 (mpp) REVERT: A 701 GLN cc_start: 0.1108 (pm20) cc_final: 0.0778 (pm20) REVERT: A 739 MET cc_start: -0.3880 (mtm) cc_final: -0.4394 (mtt) REVERT: A 921 MET cc_start: 0.1457 (mmm) cc_final: 0.1026 (mmm) REVERT: C 322 LEU cc_start: 0.7126 (tp) cc_final: 0.6659 (tp) REVERT: C 687 MET cc_start: -0.0478 (pmm) cc_final: -0.0979 (pmm) REVERT: E 221 GLU cc_start: 0.5860 (tp30) cc_final: 0.5616 (tp30) REVERT: E 840 HIS cc_start: 0.4941 (m-70) cc_final: 0.4339 (m-70) REVERT: E 1191 MET cc_start: 0.0374 (ppp) cc_final: -0.0279 (ppp) REVERT: G 301 MET cc_start: 0.2598 (tmm) cc_final: 0.2239 (tmm) REVERT: G 504 MET cc_start: -0.1651 (mtp) cc_final: -0.2066 (mtp) REVERT: G 592 MET cc_start: -0.3562 (mtm) cc_final: -0.4416 (ptp) REVERT: I 355 LYS cc_start: 0.4088 (tptt) cc_final: 0.2914 (pttt) REVERT: I 368 MET cc_start: 0.1568 (mtm) cc_final: 0.1279 (mtt) REVERT: I 687 MET cc_start: -0.0124 (ttp) cc_final: -0.2293 (ptp) REVERT: I 739 MET cc_start: -0.2702 (mpp) cc_final: -0.3112 (mpp) REVERT: I 802 LYS cc_start: -0.0185 (mmtt) cc_final: -0.2216 (mptt) REVERT: I 936 MET cc_start: -0.1584 (ttt) cc_final: -0.2037 (ttt) REVERT: I 1191 MET cc_start: -0.2364 (ttm) cc_final: -0.2584 (tpp) REVERT: J 65 MET cc_start: 0.4755 (mmp) cc_final: 0.4550 (mmp) REVERT: K 155 MET cc_start: 0.2371 (ppp) cc_final: 0.1648 (ttp) REVERT: K 160 LYS cc_start: 0.4903 (mtmt) cc_final: 0.4676 (mttt) REVERT: K 202 LEU cc_start: 0.7838 (tp) cc_final: 0.7637 (tp) REVERT: K 301 MET cc_start: 0.1219 (ptt) cc_final: 0.0962 (ptt) REVERT: K 394 LYS cc_start: 0.3625 (mmtt) cc_final: 0.3407 (mmtm) REVERT: K 449 ASN cc_start: 0.1727 (OUTLIER) cc_final: 0.0907 (t0) REVERT: K 797 MET cc_start: -0.1110 (ttt) cc_final: -0.1669 (ttm) REVERT: K 936 MET cc_start: -0.1938 (mtp) cc_final: -0.3638 (ttt) REVERT: M 206 LEU cc_start: 0.7705 (tp) cc_final: 0.7264 (tp) REVERT: M 739 MET cc_start: -0.2015 (mtm) cc_final: -0.3006 (mtm) REVERT: M 936 MET cc_start: -0.1491 (ttp) cc_final: -0.2608 (ttm) REVERT: P 26 MET cc_start: 0.5148 (mmt) cc_final: 0.4792 (mmm) REVERT: Q 59 MET cc_start: 0.6383 (ttt) cc_final: 0.5264 (ptt) REVERT: R 26 MET cc_start: -0.2821 (mpp) cc_final: -0.3039 (mpp) REVERT: T 1 MET cc_start: -0.2990 (ttm) cc_final: -0.5009 (tpp) REVERT: U 39 MET cc_start: 0.1964 (mmt) cc_final: 0.1441 (mmm) outliers start: 6 outliers final: 1 residues processed: 855 average time/residue: 0.7255 time to fit residues: 1066.2249 Evaluate side-chains 644 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 642 time to evaluate : 6.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 778 optimal weight: 5.9990 chunk 530 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 695 optimal weight: 20.0000 chunk 385 optimal weight: 7.9990 chunk 797 optimal weight: 7.9990 chunk 646 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 477 optimal weight: 20.0000 chunk 838 optimal weight: 30.0000 chunk 235 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 GLN A 468 HIS A 477 GLN A 524 HIS A 579 GLN A 614 HIS A 701 GLN A 997 GLN ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN ** C 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 886 HIS ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS ** E 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN E 477 GLN E 531 HIS E 543 ASN E 562 ASN ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 851 GLN ** E 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1095 HIS ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 565 GLN ** G 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1095 HIS ** I 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 457 HIS ** I 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 GLN I 545 GLN I 583 GLN ** I 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1121 HIS ** I1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 GLN ** K 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 420 ASN K 438 HIS ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 463 GLN K 524 HIS ** K 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1095 HIS K1224 HIS ** M 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 420 ASN ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 438 HIS ** M 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 HIS ** M 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 524 HIS M 656 HIS ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 88 HIS P 11 GLN ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 GLN ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2739 moved from start: 0.7901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 80256 Z= 0.341 Angle : 0.842 14.362 108543 Z= 0.433 Chirality : 0.047 0.306 11993 Planarity : 0.006 0.157 13790 Dihedral : 8.625 161.937 10669 Min Nonbonded Distance : 1.426 Molprobity Statistics. All-atom Clashscore : 29.31 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.58 % Favored : 91.71 % Rotamer: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % 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: -1.88 (0.08), residues: 9716 helix: -0.56 (0.09), residues: 3243 sheet: -1.84 (0.12), residues: 1645 loop : -1.44 (0.09), residues: 4828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP E1201 HIS 0.019 0.002 HIS E 183 PHE 0.053 0.003 PHE E 740 TYR 0.038 0.003 TYR C 340 ARG 0.019 0.001 ARG G 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 820 time to evaluate : 6.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 VAL cc_start: 0.6895 (t) cc_final: 0.6602 (t) REVERT: A 158 CYS cc_start: 0.7609 (m) cc_final: 0.7093 (t) REVERT: A 255 ASP cc_start: 0.6627 (t0) cc_final: 0.6169 (t0) REVERT: A 297 LEU cc_start: 0.6583 (mt) cc_final: 0.6347 (mt) REVERT: A 301 MET cc_start: 0.4882 (ptm) cc_final: 0.4583 (ptm) REVERT: A 687 MET cc_start: 0.3147 (mpp) cc_final: 0.2900 (mpp) REVERT: A 701 GLN cc_start: 0.2014 (OUTLIER) cc_final: 0.1488 (pm20) REVERT: A 739 MET cc_start: -0.3819 (mtm) cc_final: -0.4237 (mtt) REVERT: A 879 ARG cc_start: 0.3059 (mtm180) cc_final: 0.2253 (ttp80) REVERT: C 592 MET cc_start: -0.3127 (mtp) cc_final: -0.4098 (ttm) REVERT: C 687 MET cc_start: -0.0467 (pmm) cc_final: -0.1016 (pmm) REVERT: E 1191 MET cc_start: 0.0690 (ppp) cc_final: 0.0279 (ppp) REVERT: G 413 ASP cc_start: 0.4953 (m-30) cc_final: 0.4656 (m-30) REVERT: G 504 MET cc_start: -0.1181 (mtp) cc_final: -0.1713 (mtp) REVERT: G 592 MET cc_start: -0.3398 (mtm) cc_final: -0.4039 (ptp) REVERT: G 739 MET cc_start: 0.3741 (tmm) cc_final: 0.2568 (ttt) REVERT: G 1191 MET cc_start: -0.0654 (tmm) cc_final: -0.1141 (tmm) REVERT: I 306 LEU cc_start: 0.4798 (mt) cc_final: 0.4541 (tp) REVERT: I 368 MET cc_start: 0.2452 (mtm) cc_final: 0.1775 (mtt) REVERT: I 382 TYR cc_start: 0.2586 (m-80) cc_final: 0.1191 (m-10) REVERT: I 687 MET cc_start: -0.0564 (ttp) cc_final: -0.1782 (ptp) REVERT: I 739 MET cc_start: -0.2261 (mpp) cc_final: -0.2847 (mpp) REVERT: I 921 MET cc_start: -0.3838 (mtt) cc_final: -0.4129 (mtt) REVERT: I 936 MET cc_start: -0.1274 (ttt) cc_final: -0.2075 (ttt) REVERT: K 187 VAL cc_start: 0.7869 (t) cc_final: 0.7468 (t) REVERT: K 198 LYS cc_start: 0.7671 (mttm) cc_final: 0.7098 (mmtm) REVERT: K 202 LEU cc_start: 0.7966 (tp) cc_final: 0.7727 (tp) REVERT: K 797 MET cc_start: -0.1527 (ttt) cc_final: -0.2028 (ttm) REVERT: K 936 MET cc_start: -0.1804 (mtp) cc_final: -0.3796 (ttt) REVERT: M 185 VAL cc_start: 0.7813 (p) cc_final: 0.7613 (t) REVERT: M 206 LEU cc_start: 0.8209 (tp) cc_final: 0.7826 (tp) REVERT: M 321 PRO cc_start: 0.7575 (Cg_endo) cc_final: 0.7268 (Cg_exo) REVERT: M 814 MET cc_start: 0.0378 (ttt) cc_final: -0.2578 (mtt) REVERT: M 936 MET cc_start: -0.1788 (ttp) cc_final: -0.2864 (ttm) REVERT: P 26 MET cc_start: 0.5262 (mmt) cc_final: 0.4940 (mmm) REVERT: R 29 MET cc_start: -0.0833 (mmm) cc_final: -0.1176 (mmm) REVERT: T 1 MET cc_start: -0.2578 (ttm) cc_final: -0.4716 (tpp) REVERT: U 64 THR cc_start: 0.3068 (p) cc_final: 0.2857 (p) REVERT: V 1 MET cc_start: -0.0449 (ttp) cc_final: -0.0670 (ttt) outliers start: 4 outliers final: 0 residues processed: 822 average time/residue: 0.7526 time to fit residues: 1071.5078 Evaluate side-chains 602 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 601 time to evaluate : 6.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 314 optimal weight: 30.0000 chunk 841 optimal weight: 50.0000 chunk 184 optimal weight: 4.9990 chunk 548 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 935 optimal weight: 7.9990 chunk 776 optimal weight: 2.9990 chunk 433 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 309 optimal weight: 7.9990 chunk 491 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 HIS A 416 GLN A 438 HIS A 449 ASN A 463 GLN A 468 HIS A 477 GLN ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 HIS ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 ASN B 12 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN C 441 GLN ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1176 HIS ** C1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN E 171 HIS E 190 GLN E 336 ASN E 346 GLN ** E 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 605 ASN ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1163 HIS ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 ASN ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 ASN G 709 ASN ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 ASN ** I 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 463 GLN I 477 GLN I 531 HIS I 565 GLN I 614 HIS ** I 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 344 GLN ** K 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 438 HIS ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 551 ASN ** K 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 656 HIS ** K 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 ASN ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 HIS M 477 GLN M 545 GLN ** M 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 562 ASN M 579 GLN ** M1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 GLN Q 77 HIS ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 GLN ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3195 moved from start: 0.9977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.165 80256 Z= 0.398 Angle : 0.919 26.737 108543 Z= 0.472 Chirality : 0.051 0.672 11993 Planarity : 0.006 0.145 13790 Dihedral : 8.995 167.146 10669 Min Nonbonded Distance : 1.547 Molprobity Statistics. All-atom Clashscore : 33.79 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.22 % Favored : 91.08 % Rotamer: Outliers : 0.01 % Allowed : 3.17 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -2.26 (0.08), residues: 9716 helix: -0.95 (0.09), residues: 3079 sheet: -2.10 (0.11), residues: 1652 loop : -1.58 (0.09), residues: 4985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP C 404 HIS 0.025 0.002 HIS I1002 PHE 0.048 0.003 PHE Q 34 TYR 0.077 0.003 TYR C 382 ARG 0.016 0.001 ARG I 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 809 time to evaluate : 8.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.7357 (m110) cc_final: 0.6962 (m110) REVERT: A 424 LEU cc_start: 0.8094 (tp) cc_final: 0.7780 (tp) REVERT: A 491 MET cc_start: 0.7186 (tpp) cc_final: 0.6888 (tpp) REVERT: A 701 GLN cc_start: 0.1816 (pm20) cc_final: 0.1251 (pm20) REVERT: A 921 MET cc_start: 0.3835 (mmt) cc_final: 0.3373 (mmt) REVERT: A 1191 MET cc_start: -0.2298 (mtm) cc_final: -0.3847 (ttp) REVERT: C 268 SER cc_start: 0.8640 (p) cc_final: 0.8378 (p) REVERT: C 322 LEU cc_start: 0.7881 (tp) cc_final: 0.7550 (tp) REVERT: C 445 LEU cc_start: 0.6716 (mp) cc_final: 0.6490 (mp) REVERT: C 687 MET cc_start: -0.1011 (pmm) cc_final: -0.1508 (pmm) REVERT: C 1124 ARG cc_start: 0.1606 (tpm170) cc_final: -0.0252 (mmp-170) REVERT: E 232 LEU cc_start: 0.6892 (tt) cc_final: 0.6691 (tt) REVERT: G 295 LEU cc_start: 0.5941 (mp) cc_final: 0.5594 (mt) REVERT: G 301 MET cc_start: 0.3718 (tmm) cc_final: 0.3515 (tmm) REVERT: G 504 MET cc_start: -0.1259 (mtp) cc_final: -0.1800 (mtp) REVERT: G 739 MET cc_start: 0.3717 (tmm) cc_final: 0.3186 (ttt) REVERT: G 814 MET cc_start: 0.1960 (tpp) cc_final: 0.1491 (tpp) REVERT: G 1191 MET cc_start: -0.0314 (tmm) cc_final: -0.1338 (tmm) REVERT: I 144 LYS cc_start: 0.7234 (mmmt) cc_final: 0.6924 (mttm) REVERT: I 201 ASN cc_start: 0.8043 (m-40) cc_final: 0.7116 (m-40) REVERT: I 241 ILE cc_start: 0.7743 (tt) cc_final: 0.7417 (tt) REVERT: I 687 MET cc_start: -0.0184 (ttp) cc_final: -0.1406 (mpp) REVERT: I 797 MET cc_start: 0.2469 (ppp) cc_final: 0.2163 (ppp) REVERT: I 921 MET cc_start: -0.3016 (mtt) cc_final: -0.3422 (mtt) REVERT: I 936 MET cc_start: -0.1115 (ttt) cc_final: -0.2277 (ttt) REVERT: K 187 VAL cc_start: 0.8753 (t) cc_final: 0.8323 (t) REVERT: K 797 MET cc_start: -0.0864 (ttt) cc_final: -0.1118 (ttm) REVERT: K 936 MET cc_start: -0.2366 (mtp) cc_final: -0.3638 (ttt) REVERT: M 144 LYS cc_start: 0.7368 (mptt) cc_final: 0.7050 (mptt) REVERT: M 206 LEU cc_start: 0.8790 (tp) cc_final: 0.8230 (tp) REVERT: M 739 MET cc_start: -0.1931 (mtm) cc_final: -0.2294 (mtm) REVERT: M 936 MET cc_start: -0.1264 (ttp) cc_final: -0.1776 (ttm) REVERT: O 59 MET cc_start: -0.0180 (ttp) cc_final: -0.0576 (ttm) REVERT: Q 58 LYS cc_start: 0.8709 (pptt) cc_final: 0.8463 (tmmt) REVERT: Q 59 MET cc_start: 0.6885 (ttt) cc_final: 0.5939 (ptt) REVERT: U 15 ARG cc_start: 0.4376 (mmp-170) cc_final: 0.3420 (mmp80) outliers start: 1 outliers final: 1 residues processed: 810 average time/residue: 0.7282 time to fit residues: 1017.6167 Evaluate side-chains 589 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 588 time to evaluate : 6.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 902 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 533 optimal weight: 6.9990 chunk 683 optimal weight: 2.9990 chunk 529 optimal weight: 4.9990 chunk 787 optimal weight: 0.0770 chunk 522 optimal weight: 2.9990 chunk 932 optimal weight: 20.0000 chunk 583 optimal weight: 40.0000 chunk 568 optimal weight: 7.9990 chunk 430 optimal weight: 1.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS A 565 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 ASN C 579 GLN ** C1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 GLN ** E 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 HIS ** E 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 565 GLN ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 GLN ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 ASN ** I 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 477 GLN I 698 HIS K 257 GLN ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 336 ASN K 438 HIS ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 553 HIS ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 438 HIS ** M 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 HIS M 477 GLN ** M 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3056 moved from start: 1.0161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 80256 Z= 0.215 Angle : 0.712 12.094 108543 Z= 0.360 Chirality : 0.044 0.343 11993 Planarity : 0.004 0.068 13790 Dihedral : 8.293 174.354 10669 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 24.23 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.00 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -2.02 (0.08), residues: 9716 helix: -0.49 (0.09), residues: 3129 sheet: -2.09 (0.11), residues: 1799 loop : -1.53 (0.09), residues: 4788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP E 249 HIS 0.013 0.001 HIS C 497 PHE 0.037 0.002 PHE M 526 TYR 0.039 0.002 TYR I 340 ARG 0.010 0.001 ARG I 226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 794 time to evaluate : 6.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 LEU cc_start: 0.7841 (tp) cc_final: 0.7549 (tp) REVERT: A 701 GLN cc_start: 0.1602 (pm20) cc_final: 0.1385 (pm20) REVERT: A 1191 MET cc_start: -0.2424 (mtm) cc_final: -0.3909 (ttp) REVERT: C 221 GLU cc_start: 0.7072 (tp30) cc_final: 0.6634 (tm-30) REVERT: C 297 LEU cc_start: 0.7723 (pp) cc_final: 0.7127 (tt) REVERT: C 322 LEU cc_start: 0.7655 (tp) cc_final: 0.7290 (tp) REVERT: C 1124 ARG cc_start: 0.2400 (tpm170) cc_final: 0.0679 (mmp-170) REVERT: E 201 ASN cc_start: 0.7729 (m110) cc_final: 0.7103 (m110) REVERT: E 368 MET cc_start: 0.3755 (ptt) cc_final: 0.3474 (ptt) REVERT: E 372 VAL cc_start: 0.7638 (t) cc_final: 0.7217 (t) REVERT: E 739 MET cc_start: 0.1427 (tpp) cc_final: 0.0541 (ttt) REVERT: G 504 MET cc_start: -0.2400 (mtp) cc_final: -0.3118 (mtp) REVERT: G 739 MET cc_start: 0.3432 (tmm) cc_final: 0.3188 (ttt) REVERT: G 1191 MET cc_start: -0.0122 (tmm) cc_final: -0.1241 (tmm) REVERT: I 144 LYS cc_start: 0.7349 (mmmt) cc_final: 0.7089 (mttm) REVERT: I 241 ILE cc_start: 0.7629 (tt) cc_final: 0.7353 (tt) REVERT: I 372 VAL cc_start: 0.7337 (t) cc_final: 0.7045 (t) REVERT: I 687 MET cc_start: 0.0040 (ttp) cc_final: -0.1170 (mpp) REVERT: I 739 MET cc_start: -0.1735 (mpp) cc_final: -0.2108 (mpp) REVERT: I 921 MET cc_start: -0.3269 (mtt) cc_final: -0.3611 (mtt) REVERT: I 936 MET cc_start: -0.1244 (ttt) cc_final: -0.2359 (ttt) REVERT: K 155 MET cc_start: 0.6013 (ptt) cc_final: 0.5422 (ptt) REVERT: K 256 SER cc_start: 0.8018 (m) cc_final: 0.7601 (t) REVERT: K 264 THR cc_start: 0.7733 (t) cc_final: 0.7453 (t) REVERT: K 379 ILE cc_start: 0.4812 (mm) cc_final: 0.4535 (mm) REVERT: K 739 MET cc_start: -0.1694 (mtt) cc_final: -0.1919 (mtm) REVERT: K 936 MET cc_start: -0.2909 (mtp) cc_final: -0.4008 (ttt) REVERT: M 206 LEU cc_start: 0.8683 (tp) cc_final: 0.8220 (tp) REVERT: M 277 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8137 (mttp) REVERT: M 301 MET cc_start: 0.3721 (ptp) cc_final: 0.3022 (ptp) REVERT: Q 58 LYS cc_start: 0.8771 (pptt) cc_final: 0.8410 (tmmt) REVERT: Q 59 MET cc_start: 0.6651 (ttt) cc_final: 0.5771 (ptt) REVERT: R 29 MET cc_start: -0.0280 (mmm) cc_final: -0.1040 (mmp) REVERT: U 15 ARG cc_start: 0.3950 (mmp-170) cc_final: 0.3135 (mmp80) REVERT: U 64 THR cc_start: 0.4272 (p) cc_final: 0.4034 (p) outliers start: 0 outliers final: 0 residues processed: 794 average time/residue: 0.7202 time to fit residues: 993.7461 Evaluate side-chains 601 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 601 time to evaluate : 6.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 576 optimal weight: 8.9990 chunk 372 optimal weight: 0.9980 chunk 556 optimal weight: 0.8980 chunk 280 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 592 optimal weight: 30.0000 chunk 634 optimal weight: 1.9990 chunk 460 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 732 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 485 ASN E 553 HIS E 640 GLN ** E1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1176 HIS F 52 ASN G 153 HIS ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 GLN ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 562 ASN ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 477 GLN I 955 GLN ** I1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 257 GLN ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 HIS ** M 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3135 moved from start: 1.0603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 80256 Z= 0.216 Angle : 0.698 14.387 108543 Z= 0.352 Chirality : 0.043 0.347 11993 Planarity : 0.004 0.095 13790 Dihedral : 8.103 176.531 10669 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 24.33 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.85 % Favored : 91.48 % Rotamer: Outliers : 0.02 % Allowed : 1.18 % Favored : 98.79 % 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: -1.96 (0.08), residues: 9716 helix: -0.39 (0.09), residues: 3238 sheet: -2.02 (0.11), residues: 1827 loop : -1.58 (0.09), residues: 4651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 404 HIS 0.017 0.001 HIS K 153 PHE 0.043 0.002 PHE G1213 TYR 0.036 0.002 TYR I 340 ARG 0.015 0.001 ARG I 999 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 769 time to evaluate : 6.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.7893 (tt) cc_final: 0.7577 (tt) REVERT: A 227 LEU cc_start: 0.7930 (tp) cc_final: 0.7608 (tp) REVERT: A 424 LEU cc_start: 0.8035 (tp) cc_final: 0.7648 (tp) REVERT: A 701 GLN cc_start: 0.1672 (pm20) cc_final: 0.1429 (pm20) REVERT: A 1191 MET cc_start: -0.2486 (mtm) cc_final: -0.3957 (ttp) REVERT: C 155 MET cc_start: 0.5099 (ptm) cc_final: 0.4541 (ptm) REVERT: C 201 ASN cc_start: 0.7156 (m110) cc_final: 0.6443 (m110) REVERT: C 268 SER cc_start: 0.8272 (p) cc_final: 0.8037 (p) REVERT: C 297 LEU cc_start: 0.7685 (pp) cc_final: 0.7282 (tt) REVERT: C 889 MET cc_start: -0.0879 (tpt) cc_final: -0.1222 (mpp) REVERT: C 1124 ARG cc_start: 0.2444 (tpm170) cc_final: 0.0706 (mmp-170) REVERT: G 419 VAL cc_start: 0.6698 (t) cc_final: 0.6278 (t) REVERT: G 504 MET cc_start: -0.1967 (mtp) cc_final: -0.2599 (mtp) REVERT: G 739 MET cc_start: 0.3575 (tmm) cc_final: 0.3209 (ttt) REVERT: G 814 MET cc_start: 0.1345 (tpp) cc_final: 0.0827 (tpp) REVERT: G 1191 MET cc_start: -0.0043 (tmm) cc_final: -0.1135 (tmm) REVERT: I 368 MET cc_start: 0.5271 (mtm) cc_final: 0.4993 (mtm) REVERT: I 687 MET cc_start: 0.0095 (ttp) cc_final: -0.1087 (mpp) REVERT: I 739 MET cc_start: -0.1752 (mpp) cc_final: -0.2151 (mpp) REVERT: I 921 MET cc_start: -0.2989 (mtt) cc_final: -0.3354 (mtt) REVERT: I 936 MET cc_start: -0.1366 (ttt) cc_final: -0.2465 (ttt) REVERT: K 255 ASP cc_start: 0.6244 (t70) cc_final: 0.6025 (t0) REVERT: K 936 MET cc_start: -0.2894 (mtp) cc_final: -0.3722 (ttt) REVERT: M 206 LEU cc_start: 0.8666 (tp) cc_final: 0.8134 (tp) REVERT: M 277 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8316 (mttp) REVERT: M 440 LEU cc_start: 0.6611 (mt) cc_final: 0.5946 (mt) REVERT: M 936 MET cc_start: -0.1913 (ttp) cc_final: -0.2557 (ttm) REVERT: P 55 MET cc_start: 0.3903 (ptp) cc_final: 0.2964 (ptt) REVERT: Q 58 LYS cc_start: 0.8774 (pptt) cc_final: 0.8312 (tmmt) REVERT: Q 59 MET cc_start: 0.6302 (ttt) cc_final: 0.5626 (ptt) REVERT: R 29 MET cc_start: 0.0178 (mmm) cc_final: -0.0564 (mmp) REVERT: S 1 MET cc_start: 0.0461 (ttm) cc_final: 0.0084 (mtt) REVERT: U 15 ARG cc_start: 0.4032 (mmp-170) cc_final: 0.3708 (mmp80) REVERT: U 64 THR cc_start: 0.4263 (p) cc_final: 0.3948 (p) outliers start: 2 outliers final: 1 residues processed: 771 average time/residue: 0.7168 time to fit residues: 967.4353 Evaluate side-chains 593 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 592 time to evaluate : 6.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 847 optimal weight: 20.0000 chunk 892 optimal weight: 0.0070 chunk 814 optimal weight: 10.0000 chunk 868 optimal weight: 20.0000 chunk 522 optimal weight: 0.9980 chunk 378 optimal weight: 4.9990 chunk 682 optimal weight: 3.9990 chunk 266 optimal weight: 0.8980 chunk 784 optimal weight: 7.9990 chunk 821 optimal weight: 20.0000 chunk 865 optimal weight: 2.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1176 HIS ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** E 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN E 737 ASN ** E1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 562 ASN ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 477 GLN I 955 GLN ** I1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 737 ASN ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 HIS M 477 GLN ** M 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 HIS ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 GLN X 12 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3120 moved from start: 1.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 80256 Z= 0.197 Angle : 0.679 13.195 108543 Z= 0.341 Chirality : 0.043 0.306 11993 Planarity : 0.004 0.068 13790 Dihedral : 7.864 179.561 10669 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.24 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.82 (0.08), residues: 9716 helix: -0.27 (0.09), residues: 3212 sheet: -1.86 (0.11), residues: 1771 loop : -1.56 (0.09), residues: 4733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 404 HIS 0.012 0.001 HIS G 497 PHE 0.043 0.002 PHE M 526 TYR 0.037 0.002 TYR I 340 ARG 0.009 0.000 ARG I 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 772 time to evaluate : 7.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 LEU cc_start: 0.9035 (mm) cc_final: 0.8617 (mm) REVERT: A 701 GLN cc_start: 0.1648 (pm20) cc_final: 0.1397 (pm20) REVERT: A 1191 MET cc_start: -0.2647 (mtm) cc_final: -0.4013 (ttp) REVERT: C 201 ASN cc_start: 0.7108 (m110) cc_final: 0.6400 (m110) REVERT: C 268 SER cc_start: 0.7870 (p) cc_final: 0.7649 (p) REVERT: C 297 LEU cc_start: 0.7764 (pp) cc_final: 0.7085 (tt) REVERT: C 378 ASP cc_start: 0.4178 (p0) cc_final: 0.3715 (p0) REVERT: C 889 MET cc_start: -0.0494 (tpt) cc_final: -0.0780 (mpp) REVERT: G 294 ILE cc_start: 0.6098 (tp) cc_final: 0.5832 (tp) REVERT: G 396 PRO cc_start: 0.2600 (Cg_endo) cc_final: 0.2216 (Cg_exo) REVERT: G 504 MET cc_start: -0.2180 (mtp) cc_final: -0.2786 (mtp) REVERT: G 739 MET cc_start: 0.3320 (tmm) cc_final: 0.3035 (ttt) REVERT: G 814 MET cc_start: 0.1518 (tpp) cc_final: 0.0930 (tpp) REVERT: G 1191 MET cc_start: -0.0174 (tmm) cc_final: -0.0921 (tmm) REVERT: I 687 MET cc_start: 0.0184 (ttp) cc_final: -0.0870 (mpp) REVERT: I 739 MET cc_start: -0.1849 (mpp) cc_final: -0.2180 (mpp) REVERT: I 936 MET cc_start: -0.1342 (ttt) cc_final: -0.2443 (ttt) REVERT: M 206 LEU cc_start: 0.8690 (tp) cc_final: 0.8122 (tp) REVERT: M 322 LEU cc_start: 0.7984 (pt) cc_final: 0.7745 (pp) REVERT: M 375 LEU cc_start: 0.7145 (mm) cc_final: 0.6937 (mm) REVERT: M 936 MET cc_start: -0.2130 (ttp) cc_final: -0.2910 (ttm) REVERT: O 1 MET cc_start: 0.0906 (mpp) cc_final: 0.0258 (ptp) REVERT: P 55 MET cc_start: 0.4184 (ptp) cc_final: 0.3188 (ptt) REVERT: Q 58 LYS cc_start: 0.8667 (pptt) cc_final: 0.8435 (tmmt) REVERT: Q 59 MET cc_start: 0.6253 (ttt) cc_final: 0.5638 (ptt) REVERT: R 29 MET cc_start: 0.0260 (mmm) cc_final: -0.0184 (mmm) REVERT: S 1 MET cc_start: 0.0649 (ttm) cc_final: 0.0316 (mtt) REVERT: U 15 ARG cc_start: 0.3916 (mmp-170) cc_final: 0.3609 (mmp80) outliers start: 0 outliers final: 0 residues processed: 772 average time/residue: 0.7013 time to fit residues: 947.3061 Evaluate side-chains 593 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 593 time to evaluate : 6.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 570 optimal weight: 3.9990 chunk 918 optimal weight: 20.0000 chunk 560 optimal weight: 0.0870 chunk 435 optimal weight: 50.0000 chunk 638 optimal weight: 6.9990 chunk 963 optimal weight: 9.9990 chunk 886 optimal weight: 20.0000 chunk 767 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 592 optimal weight: 40.0000 chunk 470 optimal weight: 20.0000 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 201 ASN ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 ASN ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 ASN ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 565 GLN ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 ASN E 706 HIS ** E1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1043 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 531 HIS G 553 HIS G 562 ASN ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 931 GLN ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 ASN ** I 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 477 GLN I 583 GLN ** I 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN ** I1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1219 ASN I1237 ASN ** K 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 HIS M 477 GLN ** M 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 931 GLN ** M1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 65 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3430 moved from start: 1.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 80256 Z= 0.323 Angle : 0.801 13.326 108543 Z= 0.410 Chirality : 0.047 0.469 11993 Planarity : 0.005 0.156 13790 Dihedral : 8.407 169.707 10669 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 31.20 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.94 % Favored : 90.36 % Rotamer: Outliers : 0.01 % Allowed : 0.47 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.08), residues: 9716 helix: -0.78 (0.09), residues: 3296 sheet: -1.89 (0.12), residues: 1505 loop : -1.64 (0.09), residues: 4915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 404 HIS 0.018 0.002 HIS E 438 PHE 0.046 0.003 PHE K 544 TYR 0.034 0.003 TYR I 340 ARG 0.019 0.001 ARG M 226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 761 time to evaluate : 6.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.5215 (t70) cc_final: 0.4813 (t70) REVERT: A 701 GLN cc_start: 0.1038 (pm20) cc_final: 0.0740 (pm20) REVERT: C 201 ASN cc_start: 0.7327 (m110) cc_final: 0.6659 (m110) REVERT: C 268 SER cc_start: 0.8338 (p) cc_final: 0.8055 (p) REVERT: C 297 LEU cc_start: 0.7873 (pp) cc_final: 0.7209 (tt) REVERT: C 381 ASP cc_start: 0.6950 (p0) cc_final: 0.6736 (p0) REVERT: C 491 MET cc_start: 0.4929 (tmm) cc_final: 0.4303 (tmm) REVERT: E 201 ASN cc_start: 0.7536 (m-40) cc_final: 0.6362 (m-40) REVERT: E 312 SER cc_start: 0.7948 (m) cc_final: 0.7373 (t) REVERT: G 202 LEU cc_start: 0.8526 (pp) cc_final: 0.7995 (tp) REVERT: G 301 MET cc_start: 0.4000 (tmm) cc_final: 0.3482 (tmm) REVERT: G 420 ASN cc_start: 0.6623 (t0) cc_final: 0.6421 (t0) REVERT: G 1191 MET cc_start: -0.0327 (tmm) cc_final: -0.0931 (tmm) REVERT: I 158 CYS cc_start: 0.8690 (m) cc_final: 0.7620 (t) REVERT: I 196 LEU cc_start: 0.8343 (tt) cc_final: 0.8104 (tp) REVERT: I 306 LEU cc_start: 0.7035 (mt) cc_final: 0.6606 (mt) REVERT: I 350 PHE cc_start: 0.5425 (m-10) cc_final: 0.5192 (m-10) REVERT: I 415 LEU cc_start: 0.7173 (mt) cc_final: 0.6839 (mt) REVERT: I 687 MET cc_start: 0.1164 (ttp) cc_final: -0.0118 (mpp) REVERT: I 936 MET cc_start: -0.0827 (ttt) cc_final: -0.1904 (ttt) REVERT: K 687 MET cc_start: 0.3537 (mmm) cc_final: 0.2692 (mmm) REVERT: M 206 LEU cc_start: 0.8857 (tp) cc_final: 0.8459 (tp) REVERT: M 283 GLU cc_start: 0.4741 (pp20) cc_final: 0.4424 (pp20) REVERT: M 299 VAL cc_start: 0.7183 (p) cc_final: 0.6771 (t) REVERT: M 301 MET cc_start: 0.5890 (pmm) cc_final: 0.4809 (pmm) REVERT: M 936 MET cc_start: -0.1916 (ttp) cc_final: -0.2486 (ttm) REVERT: P 55 MET cc_start: 0.3998 (ptp) cc_final: 0.3046 (ptt) REVERT: P 59 MET cc_start: 0.0994 (ttp) cc_final: 0.0784 (ttt) REVERT: Q 58 LYS cc_start: 0.8720 (pptt) cc_final: 0.8395 (tmmt) REVERT: Q 59 MET cc_start: 0.6308 (ttt) cc_final: 0.5543 (ptt) REVERT: R 29 MET cc_start: -0.0281 (mmm) cc_final: -0.0837 (mmm) REVERT: U 15 ARG cc_start: 0.4149 (mmp-170) cc_final: 0.3892 (mmp80) REVERT: U 44 GLN cc_start: 0.5321 (mp10) cc_final: 0.4439 (mp10) REVERT: V 1 MET cc_start: -0.0914 (ttt) cc_final: -0.1172 (ttt) outliers start: 1 outliers final: 0 residues processed: 762 average time/residue: 0.7173 time to fit residues: 958.4820 Evaluate side-chains 572 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 572 time to evaluate : 6.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 609 optimal weight: 0.7980 chunk 817 optimal weight: 8.9990 chunk 235 optimal weight: 2.9990 chunk 707 optimal weight: 50.0000 chunk 113 optimal weight: 0.5980 chunk 213 optimal weight: 8.9990 chunk 768 optimal weight: 4.9990 chunk 321 optimal weight: 20.0000 chunk 788 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 468 HIS ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 ASN C1216 ASN ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN E 121 GLN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 706 HIS ** E1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1043 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN F 52 ASN ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 562 ASN ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 449 ASN I 477 GLN I 553 HIS ** I 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 931 GLN I 955 GLN ** I1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 346 GLN ** M 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 HIS ** M 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.124080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.106587 restraints weight = 691541.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.105155 restraints weight = 462106.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.105394 restraints weight = 408935.195| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5955 moved from start: 1.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 80256 Z= 0.215 Angle : 0.707 11.881 108543 Z= 0.357 Chirality : 0.044 0.375 11993 Planarity : 0.004 0.072 13790 Dihedral : 8.059 173.603 10669 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 25.54 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.79 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.97 (0.08), residues: 9716 helix: -0.49 (0.09), residues: 3223 sheet: -1.93 (0.11), residues: 1757 loop : -1.56 (0.09), residues: 4736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP M 483 HIS 0.016 0.001 HIS K 171 PHE 0.031 0.002 PHE M 464 TYR 0.034 0.002 TYR I 340 ARG 0.014 0.001 ARG G 434 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18736.66 seconds wall clock time: 332 minutes 45.40 seconds (19965.40 seconds total)