Starting phenix.real_space_refine on Fri Mar 15 19:18:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/03_2024/3jbt_6480_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/03_2024/3jbt_6480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/03_2024/3jbt_6480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/03_2024/3jbt_6480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/03_2024/3jbt_6480_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/03_2024/3jbt_6480_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 455 5.16 5 C 44499 2.51 5 N 12054 2.21 5 O 13209 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 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" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 70252 Number of models: 1 Model: "" Number of chains: 28 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: "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: 26.78, per 1000 atoms: 0.38 Number of scatterers: 70252 At special positions: 0 Unit cell: (306.24, 306.24, 87.12, 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 455 16.00 P 21 15.00 Mg 7 11.99 O 13209 8.00 N 12054 7.00 C 44499 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=2.19 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: 21.07 Conformation dependent library (CDL) restraints added in 9.3 seconds 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 224 helices and 126 sheets defined 26.4% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.53 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: 3.676A 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: 3.531A 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: 3.668A pdb=" N ILE A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 7.002A 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: 3.835A pdb=" N GLN A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE A 461 " --> pdb=" O HIS A 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 462 " --> pdb=" O LYS A 458 " (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: 4.079A pdb=" N PHE A 486 " --> pdb=" O TRP A 483 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ALA A 488 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 3.833A 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 516 Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.538A 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: 3.720A pdb=" N ILE A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 549 removed outlier: 3.666A 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 576 through 590 removed outlier: 3.554A pdb=" N LEU A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 589 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 4.229A 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: 4.140A 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: 3.527A 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: 3.676A 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: 3.612A pdb=" N ILE C 314 " --> pdb=" O HIS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 removed outlier: 3.831A 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: 3.531A 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: 3.712A 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: 3.823A pdb=" N ASP C 385 " --> pdb=" O ASP C 381 " (cutoff:3.500A) removed outlier: 4.095A 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: 3.669A 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: 3.835A 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: 4.006A pdb=" N LYS C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE C 461 " --> pdb=" O HIS C 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR C 462 " --> pdb=" O LYS C 458 " (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: 4.079A pdb=" N PHE C 486 " --> pdb=" O TRP C 483 " (cutoff:3.500A) removed outlier: 4.998A 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 516 Processing helix chain 'C' and resid 521 through 532 removed outlier: 3.537A 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: 3.720A pdb=" N ILE C 532 " --> pdb=" O GLU C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 549 removed outlier: 3.666A 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 576 through 590 removed outlier: 3.554A pdb=" N LEU C 582 " --> pdb=" O GLN C 578 " (cutoff:3.500A) removed outlier: 3.617A 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: 3.523A 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: 3.562A pdb=" N VAL E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 177 removed outlier: 3.526A pdb=" N GLY E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 206 removed outlier: 3.627A pdb=" N MET E 197 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 3.676A 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: 3.592A pdb=" N HIS E 311 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 3.612A 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: 3.531A pdb=" N MET E 368 " --> pdb=" O LEU E 364 " (cutoff:3.500A) removed outlier: 3.753A 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: 4.572A 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: 4.339A pdb=" N TYR E 382 " --> pdb=" O ASP E 378 " (cutoff:3.500A) removed outlier: 4.031A 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: 7.002A 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: 3.835A 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: 4.007A pdb=" N LYS E 458 " --> pdb=" O GLN E 454 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS E 459 " --> pdb=" O ASP E 455 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE E 461 " --> pdb=" O HIS E 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 494 removed outlier: 4.214A pdb=" N MET E 481 " --> pdb=" O GLU E 478 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE E 486 " --> pdb=" O TRP E 483 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ALA E 488 " --> pdb=" O ASN E 485 " (cutoff:3.500A) removed outlier: 3.833A 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 516 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: 3.720A pdb=" N ILE E 532 " --> pdb=" O GLU E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 549 removed outlier: 3.666A 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 576 through 590 removed outlier: 3.554A pdb=" N LEU E 582 " --> pdb=" O GLN E 578 " (cutoff:3.500A) removed outlier: 3.617A 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: 4.140A 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: 3.523A 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: 3.592A pdb=" N HIS G 311 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE G 314 " --> pdb=" O HIS G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 333 removed outlier: 3.831A 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: 3.531A pdb=" N MET G 368 " --> pdb=" O LEU G 364 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE G 370 " --> pdb=" O GLU G 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU G 373 " --> pdb=" O SER G 369 " (cutoff:3.500A) removed outlier: 4.571A 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: 4.031A pdb=" N THR G 384 " --> pdb=" O LYS G 380 " (cutoff:3.500A) removed outlier: 3.823A 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: 4.149A 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: 6.845A 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: 4.007A pdb=" N LYS G 458 " --> pdb=" O GLN G 454 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 459 " --> pdb=" O ASP G 455 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE G 461 " --> pdb=" O HIS G 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR G 462 " --> pdb=" O LYS G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 494 removed outlier: 4.214A pdb=" N MET G 481 " --> pdb=" O GLU G 478 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE G 486 " --> pdb=" O TRP G 483 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ALA G 488 " --> pdb=" O ASN G 485 " (cutoff:3.500A) removed outlier: 3.833A 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 516 Processing helix chain 'G' and resid 521 through 532 removed outlier: 3.538A pdb=" N GLU G 528 " --> pdb=" O HIS G 524 " (cutoff:3.500A) removed outlier: 4.268A 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 576 through 590 removed outlier: 3.553A pdb=" N LEU G 582 " --> pdb=" O GLN G 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP G 589 " --> pdb=" O LYS G 585 " (cutoff:3.500A) removed outlier: 4.228A 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: 3.562A 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: 3.627A 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: 3.592A 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: 3.831A 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: 3.754A pdb=" N ILE I 370 " --> pdb=" O GLU I 366 " (cutoff:3.500A) removed outlier: 3.618A 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: 3.712A pdb=" N ASP I 381 " --> pdb=" O GLU I 377 " (cutoff:3.500A) removed outlier: 4.339A 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: 3.823A pdb=" N ASP I 385 " --> pdb=" O ASP I 381 " (cutoff:3.500A) removed outlier: 4.096A 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: 7.003A 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: 4.007A pdb=" N LYS I 458 " --> pdb=" O GLN I 454 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS I 459 " --> pdb=" O ASP I 455 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE I 461 " --> pdb=" O HIS I 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR I 462 " --> pdb=" O LYS I 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 494 removed outlier: 4.214A pdb=" N MET I 481 " --> pdb=" O GLU I 478 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE I 486 " --> pdb=" O TRP I 483 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ALA I 488 " --> pdb=" O ASN I 485 " (cutoff:3.500A) removed outlier: 3.833A 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 516 Processing helix chain 'I' and resid 521 through 532 removed outlier: 3.538A 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: 3.720A 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 576 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: 4.140A 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: 3.523A 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: 3.562A pdb=" N VAL K 168 " --> pdb=" O ALA K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 177 removed outlier: 3.527A pdb=" N GLY K 176 " --> pdb=" O SER K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 206 removed outlier: 3.627A 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: 3.592A 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: 3.831A pdb=" N ASP K 333 " --> pdb=" O ALA K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 347 removed outlier: 3.879A 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: 3.618A pdb=" N GLU K 373 " --> pdb=" O SER K 369 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET K 374 " --> pdb=" O ILE K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 388 removed outlier: 3.712A 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: 4.030A 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: 4.149A pdb=" N ASP K 413 " --> pdb=" O GLU K 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE K 414 " --> pdb=" O GLU K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 439 through 466 removed outlier: 7.003A 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: 3.835A pdb=" N GLN K 454 " --> pdb=" O CYS K 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP K 455 " --> pdb=" O SER K 451 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS K 458 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS K 459 " --> pdb=" O ASP K 455 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE K 461 " --> pdb=" O HIS K 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR K 462 " --> pdb=" O LYS K 458 " (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: 4.078A pdb=" N PHE K 486 " --> pdb=" O TRP K 483 " (cutoff:3.500A) removed outlier: 4.999A 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 516 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: 3.719A pdb=" N ILE K 532 " --> pdb=" O GLU K 528 " (cutoff:3.500A) Processing helix chain 'K' and resid 535 through 549 removed outlier: 3.667A 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 576 through 590 removed outlier: 3.552A 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: 4.140A 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 169 removed outlier: 3.562A pdb=" N VAL M 168 " --> pdb=" O ALA M 164 " (cutoff:3.500A) 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: 3.627A 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: 3.592A pdb=" N HIS M 311 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 3.611A 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: 3.531A 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: 3.713A pdb=" N ASP M 381 " --> pdb=" O GLU M 377 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR M 382 " --> pdb=" O ASP M 378 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR M 384 " --> pdb=" O LYS M 380 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP M 385 " --> pdb=" O ASP M 381 " (cutoff:3.500A) removed outlier: 4.096A 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: 4.150A pdb=" N ASP M 413 " --> pdb=" O GLU M 409 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE M 414 " --> pdb=" O GLU M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 466 removed outlier: 7.003A 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: 3.834A pdb=" N GLN M 454 " --> pdb=" O CYS M 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP M 455 " --> pdb=" O SER M 451 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS M 458 " --> pdb=" O GLN M 454 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS M 459 " --> pdb=" O ASP M 455 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE M 461 " --> pdb=" O HIS M 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR M 462 " --> pdb=" O LYS M 458 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 494 removed outlier: 4.214A pdb=" N MET M 481 " --> pdb=" O GLU M 478 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE M 486 " --> pdb=" O TRP M 483 " (cutoff:3.500A) removed outlier: 4.999A 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 516 Processing helix chain 'M' and resid 521 through 532 removed outlier: 3.538A 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 576 through 590 removed outlier: 3.553A 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: 4.230A 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: 3.522A 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 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: 7.244A pdb=" N ILE A 260 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N ILE A 152 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.305A 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: 6.329A 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: 4.672A 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: 5.405A 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: 3.846A 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: 5.462A pdb=" N ASP A 825 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 5.463A 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: 3.791A 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: 4.001A 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: 4.522A 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: 4.423A 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: 6.771A 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: 6.324A 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: 9.100A 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: 6.352A pdb=" N LEU C 240 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR C 263 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.321A 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: 3.901A 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: 6.329A 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: 4.581A 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: 4.671A pdb=" N PHE C 707 " --> pdb=" O LEU C 715 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 715 " --> pdb=" O PHE C 707 " (cutoff:3.500A) removed outlier: 5.405A 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: 3.846A 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: 5.464A 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: 3.791A 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: 3.515A 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: 3.573A 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: 4.521A 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: 6.366A 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: 6.534A 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: 6.770A pdb=" N TRP E 149 " --> pdb=" O TYR E 278 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL E 280 " --> pdb=" O TRP E 149 " (cutoff:3.500A) removed outlier: 6.324A 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: 9.100A 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: 6.353A 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: 6.320A 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: 3.901A 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: 6.329A 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: 4.671A pdb=" N PHE E 707 " --> pdb=" O LEU E 715 " (cutoff:3.500A) removed outlier: 6.643A 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: 5.976A 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: 5.462A 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: 5.505A pdb=" N ASN E 868 " --> pdb=" O LYS E 874 " (cutoff:3.500A) removed outlier: 5.550A 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: 3.516A 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: 4.001A 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: 6.641A 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: 6.366A pdb=" N SER E 900 " --> pdb=" O HIS E 886 " (cutoff:3.500A) removed outlier: 4.424A 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: 8.180A pdb=" N VAL G 280 " --> pdb=" O TRP G 149 " (cutoff:3.500A) removed outlier: 6.325A 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: 9.100A pdb=" N ILE G 152 " --> pdb=" O ILE G 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU G 262 " --> pdb=" O ILE G 152 " (cutoff:3.500A) removed outlier: 6.353A 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: 3.902A 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: 6.329A 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: 4.581A pdb=" N CYS G 705 " --> pdb=" O ALA G 717 " (cutoff:3.500A) removed outlier: 7.263A 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: 6.643A 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: 5.550A 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: 3.516A 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: 4.001A pdb=" N ASP G1182 " --> pdb=" O ALA G1195 " (cutoff:3.500A) removed outlier: 3.573A 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: 6.642A 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: 6.680A 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: 6.367A 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: 6.769A 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: 6.324A 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: 9.100A 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: 7.747A 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: 6.329A 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: 4.671A pdb=" N PHE I 707 " --> pdb=" O LEU I 715 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU I 715 " --> pdb=" O PHE I 707 " (cutoff:3.500A) removed outlier: 5.405A 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: 3.846A 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: 5.463A 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: 3.792A 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: 3.516A 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: 3.573A 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: 6.642A 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: 6.366A 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: 6.534A 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: 6.770A pdb=" N TRP K 149 " --> pdb=" O TYR K 278 " (cutoff:3.500A) removed outlier: 8.181A 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: 7.244A pdb=" N ILE K 260 " --> pdb=" O VAL K 150 " (cutoff:3.500A) removed outlier: 9.100A 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: 6.353A 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: 6.320A 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: 6.329A 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: 4.581A 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: 4.671A 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: 5.462A pdb=" N ASP K 825 " --> pdb=" O LEU K 831 " (cutoff:3.500A) removed outlier: 5.463A 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: 5.505A 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: 3.516A 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: 4.001A pdb=" N ASP K1182 " --> pdb=" O ALA K1195 " (cutoff:3.500A) removed outlier: 3.574A 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: 6.680A 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: 6.366A pdb=" N SER K 900 " --> pdb=" O HIS K 886 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL K 888 " --> pdb=" O LEU K 898 " (cutoff:3.500A) removed outlier: 6.535A 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: 7.243A pdb=" N ILE M 260 " --> pdb=" O VAL M 150 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ILE M 152 " --> pdb=" O ILE M 260 " (cutoff:3.500A) removed outlier: 7.306A 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: 6.092A 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: 7.262A pdb=" N ALA M 717 " --> pdb=" O CYS M 705 " (cutoff:3.500A) removed outlier: 4.671A 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: 3.846A 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: 5.463A 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: 5.506A 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: 3.791A 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: 6.641A 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: 6.367A 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: 6.534A pdb=" N LEU M 898 " --> pdb=" O VAL M 888 " (cutoff:3.500A) 1876 hydrogen bonds defined for protein. 4956 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: 29.89 Time building geometry restraints manager: 23.21 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: 23823 1.37 - 1.55: 47172 1.55 - 1.74: 167 1.74 - 1.92: 623 1.92 - 2.10: 21 Bond restraints: 71806 Sorted by residual: 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 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 6.84e+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 6.82e+01 bond pdb=" C4 DTP K1301 " pdb=" C5 DTP K1301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.81e+01 ... (remaining 71801 not shown) Histogram of bond angle deviations from ideal: 85.96 - 104.38: 901 104.38 - 122.81: 86742 122.81 - 141.23: 9559 141.23 - 159.66: 0 159.66 - 178.08: 14 Bond angle restraints: 97216 Sorted by residual: angle pdb=" PB DTP E1301 " pdb=" O3B DTP E1301 " pdb=" PG DTP E1301 " ideal model delta sigma weight residual 139.87 120.50 19.37 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 139.87 120.51 19.36 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB DTP A1301 " pdb=" O3B DTP A1301 " pdb=" PG DTP A1301 " 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 I1301 " pdb=" O3B DTP I1301 " pdb=" PG DTP I1301 " ideal model delta sigma weight residual 139.87 120.54 19.33 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB DTP G1301 " pdb=" O3B DTP G1301 " pdb=" PG DTP G1301 " ideal model delta sigma weight residual 139.87 120.54 19.33 1.00e+00 1.00e+00 3.74e+02 ... (remaining 97211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.23: 38853 26.23 - 52.45: 3197 52.45 - 78.68: 860 78.68 - 104.90: 105 104.90 - 131.13: 7 Dihedral angle restraints: 43022 sinusoidal: 17619 harmonic: 25403 Sorted by residual: 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 93.00 174.16 -81.16 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS I 761 " pdb=" SG CYS I 761 " pdb=" SG CYS I 804 " pdb=" CB CYS I 804 " ideal model delta sinusoidal sigma weight residual 93.00 174.13 -81.13 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS G 761 " pdb=" SG CYS G 761 " pdb=" SG CYS G 804 " pdb=" CB CYS G 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 43019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 9238 0.096 - 0.192: 1207 0.192 - 0.289: 241 0.289 - 0.385: 31 0.385 - 0.481: 14 Chirality restraints: 10731 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 5.79e+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 C 153 " pdb=" N HIS C 153 " pdb=" C HIS C 153 " pdb=" CB HIS C 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 10728 not shown) Planarity restraints: 12306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 280 " -0.100 5.00e-02 4.00e+02 1.58e-01 3.98e+01 pdb=" N PRO A 281 " 0.273 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 280 " -0.100 5.00e-02 4.00e+02 1.58e-01 3.97e+01 pdb=" N PRO C 281 " 0.273 5.00e-02 4.00e+02 pdb=" CA PRO C 281 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO C 281 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 280 " -0.100 5.00e-02 4.00e+02 1.57e-01 3.97e+01 pdb=" N PRO E 281 " 0.273 5.00e-02 4.00e+02 pdb=" CA PRO E 281 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO E 281 " -0.082 5.00e-02 4.00e+02 ... (remaining 12303 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 1246 2.52 - 3.11: 58073 3.11 - 3.71: 108732 3.71 - 4.30: 158283 4.30 - 4.90: 246001 Nonbonded interactions: 572335 Sorted by model distance: nonbonded pdb=" O ASN D 103 " pdb=" O GLU D 104 " model vdw 1.919 3.040 nonbonded pdb=" O ASN H 103 " pdb=" O GLU H 104 " model vdw 1.919 3.040 nonbonded pdb=" O ASN B 103 " pdb=" O GLU B 104 " model vdw 1.919 3.040 nonbonded pdb=" O ASN L 103 " pdb=" O GLU L 104 " model vdw 1.919 3.040 nonbonded pdb=" O ASN N 103 " pdb=" O GLU N 104 " model vdw 1.919 3.040 ... (remaining 572330 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' } 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 9.720 Check model and map are aligned: 0.790 Set scattering table: 0.510 Process input model: 145.550 Find NCS groups from input model: 3.540 Set up NCS constraints: 0.540 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: 164.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4905 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 0.215 71806 Z= 0.504 Angle : 1.314 19.369 97216 Z= 0.923 Chirality : 0.071 0.481 10731 Planarity : 0.010 0.158 12306 Dihedral : 19.732 131.128 26453 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 70.66 Ramachandran Plot: Outliers : 3.64 % Allowed : 8.02 % Favored : 88.34 % Rotamer: Outliers : 18.24 % Allowed : 11.14 % Favored : 70.62 % Cbeta Deviations : 0.09 % 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: -0.65 (0.09), residues: 8708 helix: 0.52 (0.10), residues: 2317 sheet: -1.68 (0.16), residues: 1134 loop : -0.52 (0.09), residues: 5257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 249 HIS 0.013 0.001 HIS D 33 PHE 0.019 0.002 PHE L 82 TYR 0.038 0.003 TYR J 67 ARG 0.007 0.001 ARG N 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3247 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1421 poor density : 1826 time to evaluate : 5.861 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: A 122 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7265 (ptt180) REVERT: A 206 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7552 (tt) REVERT: A 261 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7040 (tt) REVERT: A 265 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7719 (mtt180) REVERT: A 267 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8327 (tttt) REVERT: A 311 HIS cc_start: 0.7638 (OUTLIER) cc_final: 0.7057 (t-90) REVERT: A 325 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8932 (t) REVERT: A 403 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7167 (tp) REVERT: A 457 HIS cc_start: 0.6287 (OUTLIER) cc_final: 0.5743 (m-70) REVERT: A 486 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7484 (m-80) REVERT: A 528 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6747 (tt0) REVERT: A 531 HIS cc_start: 0.5231 (OUTLIER) cc_final: 0.4830 (m-70) REVERT: A 576 VAL cc_start: 0.3485 (OUTLIER) cc_final: 0.3083 (t) REVERT: A 918 SER cc_start: -0.2905 (OUTLIER) cc_final: -0.3651 (m) REVERT: A 1220 LEU cc_start: 0.4105 (OUTLIER) cc_final: 0.2705 (tp) REVERT: A 1248 GLU cc_start: 0.4410 (OUTLIER) cc_final: 0.3586 (pt0) REVERT: B 33 HIS cc_start: 0.4336 (t70) cc_final: 0.4007 (t70) REVERT: B 80 MET cc_start: 0.4811 (ttt) cc_final: 0.4044 (ttt) REVERT: C 126 PHE cc_start: 0.6278 (OUTLIER) cc_final: 0.5740 (p90) REVERT: C 129 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8510 (mtt180) REVERT: C 206 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7274 (tt) REVERT: C 259 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: C 267 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8277 (ttpt) REVERT: C 301 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7329 (ptp) REVERT: C 345 LEU cc_start: 0.7675 (mp) cc_final: 0.7138 (mt) REVERT: C 403 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7307 (tp) REVERT: C 457 HIS cc_start: 0.6037 (OUTLIER) cc_final: 0.5826 (m-70) REVERT: C 486 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.6983 (m-80) REVERT: C 528 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6544 (tt0) REVERT: C 531 HIS cc_start: 0.5776 (OUTLIER) cc_final: 0.5440 (m-70) REVERT: C 918 SER cc_start: -0.3873 (OUTLIER) cc_final: -0.4210 (m) REVERT: C 1220 LEU cc_start: 0.3881 (OUTLIER) cc_final: 0.2791 (tp) REVERT: C 1248 GLU cc_start: 0.4617 (OUTLIER) cc_final: 0.3829 (pm20) REVERT: D 80 MET cc_start: 0.4172 (ttt) cc_final: 0.3185 (ttt) REVERT: E 114 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8429 (mt) REVERT: E 127 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7922 (m) REVERT: E 206 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7264 (tt) REVERT: E 240 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8082 (mp) REVERT: E 265 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7169 (mtt180) REVERT: E 267 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8460 (ttpt) REVERT: E 311 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.7027 (t-90) REVERT: E 528 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6393 (tt0) REVERT: E 918 SER cc_start: -0.2318 (OUTLIER) cc_final: -0.2525 (m) REVERT: E 1220 LEU cc_start: 0.4115 (OUTLIER) cc_final: 0.3253 (tp) REVERT: E 1248 GLU cc_start: 0.4795 (OUTLIER) cc_final: 0.4115 (pt0) REVERT: G 146 GLU cc_start: 0.6256 (mm-30) cc_final: 0.6025 (mm-30) REVERT: G 206 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7609 (tt) REVERT: G 259 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: G 265 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7260 (mtt180) REVERT: G 293 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7125 (tp30) REVERT: G 386 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8789 (tp) REVERT: G 403 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7064 (tp) REVERT: G 450 CYS cc_start: 0.6445 (OUTLIER) cc_final: 0.6025 (p) REVERT: G 473 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8107 (tp) REVERT: G 528 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6530 (tt0) REVERT: G 881 HIS cc_start: -0.2517 (OUTLIER) cc_final: -0.2894 (m-70) REVERT: G 918 SER cc_start: -0.3046 (OUTLIER) cc_final: -0.3443 (m) REVERT: G 1220 LEU cc_start: 0.4259 (OUTLIER) cc_final: 0.3624 (tp) REVERT: I 155 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7612 (ptm) REVERT: I 206 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7249 (tt) REVERT: I 239 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8321 (tp) REVERT: I 267 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8284 (ttpt) REVERT: I 301 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7328 (ptp) REVERT: I 457 HIS cc_start: 0.6185 (OUTLIER) cc_final: 0.5983 (m-70) REVERT: I 528 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6671 (tt0) REVERT: I 1248 GLU cc_start: 0.3997 (OUTLIER) cc_final: 0.2695 (pt0) REVERT: J 33 HIS cc_start: 0.3818 (t70) cc_final: 0.3523 (t70) REVERT: J 80 MET cc_start: 0.4610 (ttt) cc_final: 0.3799 (ttt) REVERT: K 139 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8805 (ttmm) REVERT: K 206 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7203 (tt) REVERT: K 234 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.6926 (mmtm) REVERT: K 265 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7487 (mtt180) REVERT: K 267 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8178 (ttpp) REVERT: K 403 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7039 (tp) REVERT: K 528 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6355 (tt0) REVERT: K 918 SER cc_start: -0.2871 (OUTLIER) cc_final: -0.3121 (m) REVERT: K 1193 ILE cc_start: 0.6993 (mt) cc_final: 0.6414 (mt) REVERT: K 1220 LEU cc_start: 0.4354 (OUTLIER) cc_final: 0.3684 (tp) REVERT: K 1248 GLU cc_start: 0.4689 (OUTLIER) cc_final: 0.3668 (pm20) REVERT: M 146 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6499 (mm-30) REVERT: M 240 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8223 (mp) REVERT: M 259 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: M 260 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7941 (pt) REVERT: M 261 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7055 (tt) REVERT: M 265 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7600 (mtm180) REVERT: M 267 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8272 (ttpt) REVERT: M 301 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7490 (mtm) REVERT: M 345 LEU cc_start: 0.7496 (mp) cc_final: 0.7287 (mt) REVERT: M 374 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6696 (mmt) REVERT: M 403 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7109 (tp) REVERT: M 528 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6627 (tt0) REVERT: M 531 HIS cc_start: 0.5509 (OUTLIER) cc_final: 0.5035 (m-70) REVERT: M 576 VAL cc_start: 0.3883 (OUTLIER) cc_final: 0.3075 (t) REVERT: M 918 SER cc_start: -0.2005 (OUTLIER) cc_final: -0.2494 (m) REVERT: M 1193 ILE cc_start: 0.7077 (mt) cc_final: 0.6665 (mt) REVERT: M 1220 LEU cc_start: 0.3745 (OUTLIER) cc_final: 0.3019 (tp) REVERT: M 1248 GLU cc_start: 0.4797 (OUTLIER) cc_final: 0.3747 (pm20) outliers start: 1421 outliers final: 385 residues processed: 2741 average time/residue: 0.7126 time to fit residues: 3276.6686 Evaluate side-chains 1430 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 471 poor density : 959 time to evaluate : 5.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 881 HIS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 999 ARG Chi-restraints excluded: chain A residue 1179 TRP Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1211 GLN Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1224 HIS Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1248 GLU Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 278 TYR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 303 LYS Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 438 HIS Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 450 CYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 531 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 592 MET Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 881 HIS Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 918 SER Chi-restraints excluded: chain C residue 999 ARG Chi-restraints excluded: chain C residue 1179 TRP Chi-restraints excluded: chain C residue 1181 THR Chi-restraints excluded: chain C residue 1211 GLN Chi-restraints excluded: chain C residue 1215 THR Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1224 HIS Chi-restraints excluded: chain C residue 1232 TYR Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain C residue 1248 GLU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 265 ARG Chi-restraints excluded: chain E residue 267 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 278 TYR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 334 PHE Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 374 MET Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 438 HIS Chi-restraints excluded: chain E residue 449 ASN Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 486 PHE Chi-restraints excluded: chain E residue 515 GLU Chi-restraints excluded: chain E residue 528 GLU Chi-restraints excluded: chain E residue 557 ARG Chi-restraints excluded: chain E residue 573 THR Chi-restraints excluded: chain E residue 592 MET Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 881 HIS Chi-restraints excluded: chain E residue 882 LEU Chi-restraints excluded: chain E residue 885 VAL Chi-restraints excluded: chain E residue 918 SER Chi-restraints excluded: chain E residue 999 ARG Chi-restraints excluded: chain E residue 1179 TRP Chi-restraints excluded: chain E residue 1181 THR Chi-restraints excluded: chain E residue 1211 GLN Chi-restraints excluded: chain E residue 1215 THR Chi-restraints excluded: chain E residue 1218 THR Chi-restraints excluded: chain E residue 1220 LEU Chi-restraints excluded: chain E residue 1224 HIS Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain E residue 1248 GLU Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 265 ARG Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 278 TYR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 301 MET Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 334 PHE Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 374 MET Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 439 ASP Chi-restraints excluded: chain G residue 449 ASN Chi-restraints excluded: chain G residue 450 CYS Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 528 GLU Chi-restraints excluded: chain G residue 531 HIS Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 557 ARG Chi-restraints excluded: chain G residue 573 THR Chi-restraints excluded: chain G residue 592 MET Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 882 LEU Chi-restraints excluded: chain G residue 885 VAL Chi-restraints excluded: chain G residue 907 ARG Chi-restraints excluded: chain G residue 918 SER Chi-restraints excluded: chain G residue 999 ARG Chi-restraints excluded: chain G residue 1179 TRP Chi-restraints excluded: chain G residue 1181 THR Chi-restraints excluded: chain G residue 1211 GLN Chi-restraints excluded: chain G residue 1215 THR Chi-restraints excluded: chain G residue 1218 THR Chi-restraints excluded: chain G residue 1220 LEU Chi-restraints excluded: chain G residue 1224 HIS Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1248 GLU Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 122 ARG Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 155 MET Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 237 ARG Chi-restraints excluded: chain I residue 239 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 248 SER Chi-restraints excluded: chain I residue 259 GLN Chi-restraints excluded: chain I residue 260 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 265 ARG Chi-restraints excluded: chain I residue 267 LYS Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 277 LYS Chi-restraints excluded: chain I residue 278 TYR Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 301 MET Chi-restraints excluded: chain I residue 308 GLU Chi-restraints excluded: chain I residue 317 CYS Chi-restraints excluded: chain I residue 318 LYS Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain I residue 334 PHE Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 374 MET Chi-restraints excluded: chain I residue 384 THR Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 449 ASN Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 457 HIS Chi-restraints excluded: chain I residue 528 GLU Chi-restraints excluded: chain I residue 531 HIS Chi-restraints excluded: chain I residue 573 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 881 HIS Chi-restraints excluded: chain I residue 882 LEU Chi-restraints excluded: chain I residue 999 ARG Chi-restraints excluded: chain I residue 1179 TRP Chi-restraints excluded: chain I residue 1181 THR Chi-restraints excluded: chain I residue 1211 GLN Chi-restraints excluded: chain I residue 1218 THR Chi-restraints excluded: chain I residue 1224 HIS Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain I residue 1248 GLU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain K residue 138 GLN Chi-restraints excluded: chain K residue 139 LYS Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 155 MET Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 206 LEU Chi-restraints excluded: chain K residue 234 LYS Chi-restraints excluded: chain K residue 237 ARG Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 241 ILE Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 259 GLN Chi-restraints excluded: chain K residue 260 ILE Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 265 ARG Chi-restraints excluded: chain K residue 267 LYS Chi-restraints excluded: chain K residue 277 LYS Chi-restraints excluded: chain K residue 278 TYR Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 295 LEU Chi-restraints excluded: chain K residue 301 MET Chi-restraints excluded: chain K residue 303 LYS Chi-restraints excluded: chain K residue 308 GLU Chi-restraints excluded: chain K residue 311 HIS Chi-restraints excluded: chain K residue 317 CYS Chi-restraints excluded: chain K residue 318 LYS Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain K residue 334 PHE Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 358 SER Chi-restraints excluded: chain K residue 374 MET Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 403 LEU Chi-restraints excluded: chain K residue 429 ASN Chi-restraints excluded: chain K residue 449 ASN Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 473 LEU Chi-restraints excluded: chain K residue 485 ASN Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain K residue 528 GLU Chi-restraints excluded: chain K residue 531 HIS Chi-restraints excluded: chain K residue 533 LEU Chi-restraints excluded: chain K residue 557 ARG Chi-restraints excluded: chain K residue 573 THR Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain K residue 881 HIS Chi-restraints excluded: chain K residue 882 LEU Chi-restraints excluded: chain K residue 918 SER Chi-restraints excluded: chain K residue 999 ARG Chi-restraints excluded: chain K residue 1170 GLU Chi-restraints excluded: chain K residue 1179 TRP Chi-restraints excluded: chain K residue 1181 THR Chi-restraints excluded: chain K residue 1211 GLN Chi-restraints excluded: chain K residue 1215 THR Chi-restraints excluded: chain K residue 1218 THR Chi-restraints excluded: chain K residue 1220 LEU Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain K residue 1248 GLU Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 116 GLU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 155 MET Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 189 LYS Chi-restraints excluded: chain M residue 231 MET Chi-restraints excluded: chain M residue 237 ARG Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain M residue 248 SER Chi-restraints excluded: chain M residue 252 LYS Chi-restraints excluded: chain M residue 259 GLN Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 265 ARG Chi-restraints excluded: chain M residue 267 LYS Chi-restraints excluded: chain M residue 277 LYS Chi-restraints excluded: chain M residue 278 TYR Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 301 MET Chi-restraints excluded: chain M residue 303 LYS Chi-restraints excluded: chain M residue 308 GLU Chi-restraints excluded: chain M residue 317 CYS Chi-restraints excluded: chain M residue 318 LYS Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 334 PHE Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 358 SER Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 449 ASN Chi-restraints excluded: chain M residue 450 CYS Chi-restraints excluded: chain M residue 456 LEU Chi-restraints excluded: chain M residue 486 PHE Chi-restraints excluded: chain M residue 528 GLU Chi-restraints excluded: chain M residue 530 ARG Chi-restraints excluded: chain M residue 531 HIS Chi-restraints excluded: chain M residue 533 LEU Chi-restraints excluded: chain M residue 573 THR Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain M residue 881 HIS Chi-restraints excluded: chain M residue 882 LEU Chi-restraints excluded: chain M residue 918 SER Chi-restraints excluded: chain M residue 999 ARG Chi-restraints excluded: chain M residue 1170 GLU Chi-restraints excluded: chain M residue 1179 TRP Chi-restraints excluded: chain M residue 1181 THR Chi-restraints excluded: chain M residue 1211 GLN Chi-restraints excluded: chain M residue 1218 THR Chi-restraints excluded: chain M residue 1220 LEU Chi-restraints excluded: chain M residue 1224 HIS Chi-restraints excluded: chain M residue 1232 TYR Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain M residue 1248 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 732 optimal weight: 7.9990 chunk 657 optimal weight: 1.9990 chunk 365 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 443 optimal weight: 2.9990 chunk 351 optimal weight: 20.0000 chunk 680 optimal weight: 40.0000 chunk 263 optimal weight: 0.6980 chunk 413 optimal weight: 6.9990 chunk 506 optimal weight: 1.9990 chunk 788 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 183 HIS A 201 ASN A 219 ASN A 259 GLN A 347 ASN A 420 ASN A 438 HIS ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 HIS A 485 ASN A 583 GLN A 709 ASN A 881 HIS ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 HIS A1237 ASN B 52 ASN C 137 GLN C 183 HIS C 200 GLN C 201 ASN C 219 ASN C 347 ASN C 420 ASN C 438 HIS ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** C 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 ASN C1224 HIS C1237 ASN ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 183 HIS E 200 GLN E 201 ASN E 219 ASN E 347 ASN E 420 ASN E 438 HIS ** E 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 457 HIS E 471 HIS E 583 GLN ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 ASN ** E 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1224 HIS E1237 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN G 183 HIS G 200 GLN G 201 ASN G 219 ASN G 257 GLN G 259 GLN G 347 ASN G 420 ASN G 438 HIS ** G 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 HIS G 471 HIS G 477 GLN G 583 GLN G 709 ASN ** G 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1224 HIS G1237 ASN ** H 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN I 183 HIS I 200 GLN I 201 ASN I 219 ASN I 257 GLN I 259 GLN I 347 ASN I 420 ASN I 438 HIS I 471 HIS I 545 GLN I 583 GLN ** I 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 709 ASN ** I 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1237 ASN K 137 GLN K 183 HIS K 200 GLN K 201 ASN K 257 GLN K 259 GLN K 347 ASN K 420 ASN K 429 ASN ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 457 HIS K 471 HIS K 485 ASN K 583 GLN ** K 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 709 ASN K 881 HIS ** K 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 933 ASN K1224 HIS ** K1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN M 137 GLN M 183 HIS M 200 GLN M 201 ASN M 219 ASN M 259 GLN M 347 ASN M 420 ASN ** M 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 457 HIS M 471 HIS M 583 GLN M 709 ASN ** M 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 933 ASN M1224 HIS M1237 ASN ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN Total number of N/Q/H flips: 110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5195 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 71806 Z= 0.338 Angle : 0.849 16.329 97216 Z= 0.438 Chirality : 0.048 0.432 10731 Planarity : 0.005 0.060 12306 Dihedral : 14.067 116.431 10640 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 1.03 % Allowed : 7.11 % Favored : 91.86 % Rotamer: Outliers : 8.47 % Allowed : 16.52 % Favored : 75.01 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.09), residues: 8708 helix: 0.65 (0.10), residues: 2275 sheet: -1.43 (0.13), residues: 1554 loop : -0.97 (0.09), residues: 4879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 684 HIS 0.013 0.002 HIS M 457 PHE 0.034 0.002 PHE E 526 TYR 0.032 0.003 TYR J 97 ARG 0.009 0.001 ARG M 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1735 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 660 poor density : 1075 time to evaluate : 5.851 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: A 206 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7614 (tt) REVERT: A 261 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8605 (tt) REVERT: A 353 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8642 (mt) REVERT: A 576 VAL cc_start: 0.5049 (OUTLIER) cc_final: 0.4781 (t) REVERT: A 784 LYS cc_start: 0.5099 (mmtt) cc_final: 0.4700 (mmtt) REVERT: A 847 ASP cc_start: 0.5360 (t0) cc_final: 0.5080 (t0) REVERT: B 80 MET cc_start: 0.3278 (ttt) cc_final: 0.2570 (ttt) REVERT: C 206 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7424 (tt) REVERT: C 240 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8275 (mt) REVERT: C 259 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7646 (pt0) REVERT: C 261 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8541 (pp) REVERT: C 301 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6748 (mtm) REVERT: C 327 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8822 (mm) REVERT: D 19 THR cc_start: 0.5293 (p) cc_final: 0.4780 (p) REVERT: E 261 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8706 (pp) REVERT: E 267 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8370 (ttpt) REVERT: E 301 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7274 (mtp) REVERT: E 1192 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.5742 (pp) REVERT: F 19 THR cc_start: 0.5350 (p) cc_final: 0.4975 (p) REVERT: G 163 LEU cc_start: 0.9382 (mm) cc_final: 0.9167 (mm) REVERT: G 294 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8077 (mt) REVERT: G 322 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8069 (tm) REVERT: G 330 LEU cc_start: 0.8766 (tp) cc_final: 0.8445 (mt) REVERT: G 332 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7879 (ttp-170) REVERT: G 353 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8324 (mt) REVERT: G 882 LEU cc_start: -0.2243 (OUTLIER) cc_final: -0.2591 (mm) REVERT: G 918 SER cc_start: -0.1807 (OUTLIER) cc_final: -0.2377 (m) REVERT: H 12 GLN cc_start: 0.6789 (tm-30) cc_final: 0.6580 (tm-30) REVERT: H 22 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.6072 (mtpt) REVERT: I 240 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8470 (mt) REVERT: I 261 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8632 (pp) REVERT: I 267 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8253 (ttpt) REVERT: I 441 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: I 517 VAL cc_start: 0.8596 (t) cc_final: 0.8384 (t) REVERT: I 784 LYS cc_start: 0.6050 (mmtt) cc_final: 0.5380 (mmtt) REVERT: I 921 MET cc_start: 0.0845 (mtt) cc_final: 0.0265 (mtt) REVERT: I 1192 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.6019 (pp) REVERT: J 4 GLU cc_start: 0.6216 (tp30) cc_final: 0.5934 (tp30) REVERT: K 130 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7517 (pttm) REVERT: K 261 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8962 (pp) REVERT: K 267 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8401 (ttpt) REVERT: K 294 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.8004 (tt) REVERT: K 301 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6810 (mtm) REVERT: K 353 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8563 (mt) REVERT: K 412 GLU cc_start: 0.7572 (tt0) cc_final: 0.7272 (tt0) REVERT: K 516 LEU cc_start: 0.7293 (pt) cc_final: 0.6923 (pt) REVERT: M 240 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8449 (mp) REVERT: M 261 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8770 (pp) REVERT: M 267 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8238 (ttpt) REVERT: M 353 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8395 (mt) REVERT: M 374 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6878 (mmt) REVERT: M 847 ASP cc_start: 0.5100 (t70) cc_final: 0.4830 (t70) outliers start: 660 outliers final: 309 residues processed: 1589 average time/residue: 0.6230 time to fit residues: 1720.0233 Evaluate side-chains 1123 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 777 time to evaluate : 5.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 1179 TRP Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 438 HIS Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 549 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 600 LYS Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 889 MET Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1179 TRP Chi-restraints excluded: chain C residue 1181 THR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 267 LYS Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 298 PHE Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 374 MET Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 438 HIS Chi-restraints excluded: chain E residue 449 ASN Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 524 HIS Chi-restraints excluded: chain E residue 528 GLU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 658 ASP Chi-restraints excluded: chain E residue 663 CYS Chi-restraints excluded: chain E residue 884 TRP Chi-restraints excluded: chain E residue 1179 TRP Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 401 CYS Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 449 ASN Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 491 MET Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 524 HIS Chi-restraints excluded: chain G residue 576 VAL Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 658 ASP Chi-restraints excluded: chain G residue 663 CYS Chi-restraints excluded: chain G residue 882 LEU Chi-restraints excluded: chain G residue 918 SER Chi-restraints excluded: chain G residue 1179 TRP Chi-restraints excluded: chain G residue 1181 THR Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1248 GLU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 244 ASP Chi-restraints excluded: chain I residue 248 SER Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 265 ARG Chi-restraints excluded: chain I residue 267 LYS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 298 PHE Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain I residue 370 ILE Chi-restraints excluded: chain I residue 374 MET Chi-restraints excluded: chain I residue 385 ASP Chi-restraints excluded: chain I residue 401 CYS Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 422 SER Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain I residue 449 ASN Chi-restraints excluded: chain I residue 450 CYS Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 639 LEU Chi-restraints excluded: chain I residue 663 CYS Chi-restraints excluded: chain I residue 882 LEU Chi-restraints excluded: chain I residue 918 SER Chi-restraints excluded: chain I residue 1179 TRP Chi-restraints excluded: chain I residue 1181 THR Chi-restraints excluded: chain I residue 1192 LEU Chi-restraints excluded: chain I residue 1224 HIS Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain K residue 130 LYS Chi-restraints excluded: chain K residue 138 GLN Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 259 GLN Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 267 LYS Chi-restraints excluded: chain K residue 274 MET Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 295 LEU Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 301 MET Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 358 SER Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 445 LEU Chi-restraints excluded: chain K residue 449 ASN Chi-restraints excluded: chain K residue 450 CYS Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 524 HIS Chi-restraints excluded: chain K residue 557 ARG Chi-restraints excluded: chain K residue 576 VAL Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 658 ASP Chi-restraints excluded: chain K residue 663 CYS Chi-restraints excluded: chain K residue 882 LEU Chi-restraints excluded: chain K residue 885 VAL Chi-restraints excluded: chain K residue 918 SER Chi-restraints excluded: chain K residue 1055 ASN Chi-restraints excluded: chain K residue 1170 GLU Chi-restraints excluded: chain K residue 1179 TRP Chi-restraints excluded: chain K residue 1181 THR Chi-restraints excluded: chain K residue 1199 ILE Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 248 SER Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 267 LYS Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 303 LYS Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 358 SER Chi-restraints excluded: chain M residue 360 ASP Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 401 CYS Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 422 SER Chi-restraints excluded: chain M residue 449 ASN Chi-restraints excluded: chain M residue 450 CYS Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 524 HIS Chi-restraints excluded: chain M residue 528 GLU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 600 LYS Chi-restraints excluded: chain M residue 624 SER Chi-restraints excluded: chain M residue 630 ILE Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 663 CYS Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 882 LEU Chi-restraints excluded: chain M residue 918 SER Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1170 GLU Chi-restraints excluded: chain M residue 1179 TRP Chi-restraints excluded: chain M residue 1199 ILE Chi-restraints excluded: chain M residue 1229 PHE Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 58 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 438 optimal weight: 30.0000 chunk 244 optimal weight: 8.9990 chunk 656 optimal weight: 0.0030 chunk 536 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 789 optimal weight: 10.0000 chunk 853 optimal weight: 8.9990 chunk 703 optimal weight: 20.0000 chunk 783 optimal weight: 7.9990 chunk 269 optimal weight: 0.4980 chunk 633 optimal weight: 0.9990 overall best weight: 2.2996 ------------------------------------------------------------------------------- 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 200 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 HIS A 562 ASN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN A 933 ASN B 42 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN D 42 GLN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN E 904 GLN E 933 ASN F 42 GLN ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 471 HIS G 562 ASN ** G 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 904 GLN G 933 ASN ** G1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 562 ASN ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 904 GLN I 933 ASN I1001 GLN ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1163 HIS ** I1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 441 GLN ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 471 HIS K 562 ASN K 904 GLN L 42 GLN ** M 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 471 HIS M 545 GLN ** M 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 565 GLN ** M 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 904 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5276 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 71806 Z= 0.281 Angle : 0.734 13.270 97216 Z= 0.375 Chirality : 0.044 0.259 10731 Planarity : 0.004 0.064 12306 Dihedral : 11.194 114.546 9949 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.64 % Favored : 91.56 % Rotamer: Outliers : 6.71 % Allowed : 18.52 % Favored : 74.77 % 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: -1.15 (0.09), residues: 8708 helix: 0.59 (0.11), residues: 2331 sheet: -1.47 (0.12), residues: 1659 loop : -1.16 (0.09), residues: 4718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP K1202 HIS 0.010 0.001 HIS A 471 PHE 0.033 0.002 PHE C 526 TYR 0.028 0.002 TYR J 97 ARG 0.036 0.001 ARG E 999 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1366 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 523 poor density : 843 time to evaluate : 5.963 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: A 261 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8678 (tt) REVERT: A 267 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8363 (ttpp) REVERT: A 406 MET cc_start: 0.5843 (ptm) cc_final: 0.5577 (ptm) REVERT: A 784 LYS cc_start: 0.5359 (mmtt) cc_final: 0.4584 (mmtt) REVERT: A 814 MET cc_start: 0.1129 (mmt) cc_final: 0.0911 (mmt) REVERT: B 65 MET cc_start: 0.4147 (OUTLIER) cc_final: 0.3836 (tpt) REVERT: B 80 MET cc_start: 0.3216 (ttt) cc_final: 0.2609 (ttt) REVERT: C 129 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8408 (mtt180) REVERT: C 160 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.8754 (ttmt) REVERT: C 240 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8227 (mt) REVERT: C 267 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8333 (ttpt) REVERT: C 332 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.8047 (ttp-170) REVERT: C 528 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6360 (pt0) REVERT: D 65 MET cc_start: 0.3209 (tpt) cc_final: 0.2973 (mmt) REVERT: D 82 PHE cc_start: 0.1087 (t80) cc_final: 0.0787 (t80) REVERT: E 326 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8828 (tp) REVERT: G 332 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8114 (ttp-170) REVERT: G 333 ASP cc_start: 0.7123 (m-30) cc_final: 0.6890 (m-30) REVERT: G 918 SER cc_start: -0.2042 (OUTLIER) cc_final: -0.2658 (m) REVERT: G 921 MET cc_start: 0.0655 (mtt) cc_final: 0.0336 (mtt) REVERT: G 925 GLU cc_start: 0.5533 (OUTLIER) cc_final: 0.5113 (mp0) REVERT: H 12 GLN cc_start: 0.6804 (tm-30) cc_final: 0.6590 (tm-30) REVERT: I 261 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9039 (pp) REVERT: I 439 ASP cc_start: 0.4273 (t0) cc_final: 0.4054 (t0) REVERT: I 784 LYS cc_start: 0.5332 (mmtt) cc_final: 0.4714 (mmtt) REVERT: K 130 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7392 (pttm) REVERT: K 160 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8670 (ttmt) REVERT: K 261 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9203 (pp) REVERT: K 332 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7956 (ttp-170) REVERT: K 406 MET cc_start: 0.6331 (ptm) cc_final: 0.6042 (ptm) REVERT: K 412 GLU cc_start: 0.7611 (tt0) cc_final: 0.7268 (tt0) REVERT: K 439 ASP cc_start: 0.4811 (t0) cc_final: 0.4417 (t0) REVERT: L 65 MET cc_start: 0.6027 (tmm) cc_final: 0.5270 (mmt) REVERT: M 115 CYS cc_start: 0.6931 (m) cc_final: 0.6501 (m) REVERT: M 353 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8331 (mt) REVERT: M 374 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7165 (mmt) REVERT: M 687 MET cc_start: 0.4087 (tpp) cc_final: 0.3879 (tpp) outliers start: 523 outliers final: 335 residues processed: 1257 average time/residue: 0.6060 time to fit residues: 1338.8108 Evaluate side-chains 1071 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 716 time to evaluate : 5.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1179 TRP Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1224 HIS Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 418 PHE Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 438 HIS Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 504 MET Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1055 ASN Chi-restraints excluded: chain C residue 1153 ILE Chi-restraints excluded: chain C residue 1179 TRP Chi-restraints excluded: chain C residue 1181 THR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1224 HIS Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 298 PHE Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 374 MET Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 418 PHE Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 524 HIS Chi-restraints excluded: chain E residue 542 GLU Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 653 ILE Chi-restraints excluded: chain E residue 663 CYS Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain E residue 712 HIS Chi-restraints excluded: chain E residue 803 CYS Chi-restraints excluded: chain E residue 846 CYS Chi-restraints excluded: chain E residue 884 TRP Chi-restraints excluded: chain E residue 940 VAL Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1179 TRP Chi-restraints excluded: chain E residue 1224 HIS Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 401 CYS Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 418 PHE Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 507 LEU Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 524 HIS Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 576 VAL Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 616 ASP Chi-restraints excluded: chain G residue 663 CYS Chi-restraints excluded: chain G residue 846 CYS Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 890 PHE Chi-restraints excluded: chain G residue 918 SER Chi-restraints excluded: chain G residue 925 GLU Chi-restraints excluded: chain G residue 940 VAL Chi-restraints excluded: chain G residue 999 ARG Chi-restraints excluded: chain G residue 1007 TRP Chi-restraints excluded: chain G residue 1179 TRP Chi-restraints excluded: chain G residue 1224 HIS Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1248 GLU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 248 SER Chi-restraints excluded: chain I residue 260 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 265 ARG Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 274 MET Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 298 PHE Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain I residue 385 ASP Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 401 CYS Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 418 PHE Chi-restraints excluded: chain I residue 422 SER Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 450 CYS Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 576 VAL Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 630 ILE Chi-restraints excluded: chain I residue 663 CYS Chi-restraints excluded: chain I residue 675 CYS Chi-restraints excluded: chain I residue 803 CYS Chi-restraints excluded: chain I residue 846 CYS Chi-restraints excluded: chain I residue 847 ASP Chi-restraints excluded: chain I residue 882 LEU Chi-restraints excluded: chain I residue 918 SER Chi-restraints excluded: chain I residue 940 VAL Chi-restraints excluded: chain I residue 999 ARG Chi-restraints excluded: chain I residue 1007 TRP Chi-restraints excluded: chain I residue 1179 TRP Chi-restraints excluded: chain I residue 1214 TYR Chi-restraints excluded: chain I residue 1234 THR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain K residue 130 LYS Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 264 THR Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain K residue 358 SER Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 418 PHE Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain K residue 445 LEU Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 504 MET Chi-restraints excluded: chain K residue 506 SER Chi-restraints excluded: chain K residue 517 VAL Chi-restraints excluded: chain K residue 524 HIS Chi-restraints excluded: chain K residue 534 ASP Chi-restraints excluded: chain K residue 576 VAL Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 630 ILE Chi-restraints excluded: chain K residue 663 CYS Chi-restraints excluded: chain K residue 675 CYS Chi-restraints excluded: chain K residue 803 CYS Chi-restraints excluded: chain K residue 846 CYS Chi-restraints excluded: chain K residue 882 LEU Chi-restraints excluded: chain K residue 890 PHE Chi-restraints excluded: chain K residue 918 SER Chi-restraints excluded: chain K residue 925 GLU Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1055 ASN Chi-restraints excluded: chain K residue 1153 ILE Chi-restraints excluded: chain K residue 1179 TRP Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 248 SER Chi-restraints excluded: chain M residue 252 LYS Chi-restraints excluded: chain M residue 259 GLN Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 303 LYS Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 358 SER Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 401 CYS Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 418 PHE Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 528 GLU Chi-restraints excluded: chain M residue 534 ASP Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 616 ASP Chi-restraints excluded: chain M residue 624 SER Chi-restraints excluded: chain M residue 663 CYS Chi-restraints excluded: chain M residue 675 CYS Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 846 CYS Chi-restraints excluded: chain M residue 882 LEU Chi-restraints excluded: chain M residue 918 SER Chi-restraints excluded: chain M residue 940 VAL Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1153 ILE Chi-restraints excluded: chain M residue 1179 TRP Chi-restraints excluded: chain M residue 1224 HIS Chi-restraints excluded: chain M residue 1229 PHE Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 85 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 780 optimal weight: 0.0770 chunk 593 optimal weight: 30.0000 chunk 409 optimal weight: 0.0370 chunk 87 optimal weight: 50.0000 chunk 376 optimal weight: 0.9980 chunk 530 optimal weight: 2.9990 chunk 792 optimal weight: 10.0000 chunk 839 optimal weight: 30.0000 chunk 414 optimal weight: 8.9990 chunk 751 optimal weight: 0.9990 chunk 226 optimal weight: 30.0000 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 ASN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN C 477 GLN C 562 ASN C 565 GLN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 HIS E 449 ASN E 562 ASN E 737 ASN ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 449 ASN G 562 ASN G 565 GLN ** G 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1176 HIS ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 449 ASN ** I 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 565 GLN ** K 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 449 ASN M 562 ASN ** M 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1176 HIS ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5234 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 71806 Z= 0.191 Angle : 0.663 11.562 97216 Z= 0.337 Chirality : 0.042 0.183 10731 Planarity : 0.004 0.065 12306 Dihedral : 9.970 104.169 9805 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.33 % Favored : 91.95 % Rotamer: Outliers : 5.78 % Allowed : 19.48 % Favored : 74.74 % 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: -1.23 (0.09), residues: 8708 helix: 0.57 (0.11), residues: 2352 sheet: -1.56 (0.12), residues: 1708 loop : -1.22 (0.09), residues: 4648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I1202 HIS 0.008 0.001 HIS D 33 PHE 0.036 0.001 PHE E 526 TYR 0.025 0.002 TYR N 97 ARG 0.008 0.000 ARG E 999 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 450 poor density : 804 time to evaluate : 6.051 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: A 146 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6597 (mm-30) REVERT: A 261 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8848 (tt) REVERT: A 267 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8241 (ttpp) REVERT: B 65 MET cc_start: 0.4054 (OUTLIER) cc_final: 0.3709 (tpt) REVERT: C 129 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8437 (mtt180) REVERT: C 267 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8272 (ttpp) REVERT: C 298 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8675 (t80) REVERT: D 19 THR cc_start: 0.5123 (p) cc_final: 0.4588 (p) REVERT: D 80 MET cc_start: 0.2115 (tpt) cc_final: 0.1728 (tpt) REVERT: D 82 PHE cc_start: 0.1299 (t80) cc_final: 0.0731 (t80) REVERT: E 160 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8533 (mmmm) REVERT: E 326 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8651 (tp) REVERT: E 491 MET cc_start: 0.6640 (pmm) cc_final: 0.6346 (pmm) REVERT: F 19 THR cc_start: 0.5392 (p) cc_final: 0.5062 (p) REVERT: G 252 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8417 (tptp) REVERT: G 925 GLU cc_start: 0.5590 (OUTLIER) cc_final: 0.5223 (mp0) REVERT: H 12 GLN cc_start: 0.6812 (tm-30) cc_final: 0.6554 (tm-30) REVERT: I 261 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9182 (tt) REVERT: I 784 LYS cc_start: 0.5678 (mmtt) cc_final: 0.5235 (mmtt) REVERT: J 19 THR cc_start: 0.5159 (p) cc_final: 0.4903 (p) REVERT: K 126 PHE cc_start: 0.6772 (OUTLIER) cc_final: 0.6028 (p90) REVERT: K 160 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8424 (ttmt) REVERT: K 261 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9066 (pp) REVERT: K 332 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7985 (ttp-170) REVERT: K 439 ASP cc_start: 0.4655 (t0) cc_final: 0.4121 (t0) REVERT: L 19 THR cc_start: 0.5705 (p) cc_final: 0.5352 (p) REVERT: L 22 LYS cc_start: 0.4492 (OUTLIER) cc_final: 0.4262 (mmmm) REVERT: L 65 MET cc_start: 0.6046 (tmm) cc_final: 0.5194 (mmt) REVERT: L 80 MET cc_start: 0.3129 (tpt) cc_final: 0.2877 (tpt) REVERT: M 115 CYS cc_start: 0.6937 (m) cc_final: 0.6471 (m) outliers start: 450 outliers final: 288 residues processed: 1161 average time/residue: 0.6022 time to fit residues: 1231.1850 Evaluate side-chains 1031 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 727 time to evaluate : 5.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 889 MET Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1224 HIS Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 418 PHE Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 803 CYS Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 918 SER Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1055 ASN Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1224 HIS Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 298 PHE Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 418 PHE Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 524 HIS Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 653 ILE Chi-restraints excluded: chain E residue 663 CYS Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain E residue 712 HIS Chi-restraints excluded: chain E residue 803 CYS Chi-restraints excluded: chain E residue 846 CYS Chi-restraints excluded: chain E residue 940 VAL Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1224 HIS Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain F residue 74 TYR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 401 CYS Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 418 PHE Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 507 LEU Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 524 HIS Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 576 VAL Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 663 CYS Chi-restraints excluded: chain G residue 846 CYS Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 890 PHE Chi-restraints excluded: chain G residue 925 GLU Chi-restraints excluded: chain G residue 940 VAL Chi-restraints excluded: chain G residue 1007 TRP Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1248 GLU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 260 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain I residue 265 ARG Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 298 PHE Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain I residue 385 ASP Chi-restraints excluded: chain I residue 401 CYS Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 418 PHE Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 576 VAL Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 663 CYS Chi-restraints excluded: chain I residue 803 CYS Chi-restraints excluded: chain I residue 846 CYS Chi-restraints excluded: chain I residue 882 LEU Chi-restraints excluded: chain I residue 940 VAL Chi-restraints excluded: chain I residue 1007 TRP Chi-restraints excluded: chain I residue 1055 ASN Chi-restraints excluded: chain I residue 1214 TYR Chi-restraints excluded: chain I residue 1234 THR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 327 ILE Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 418 PHE Chi-restraints excluded: chain K residue 445 LEU Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 504 MET Chi-restraints excluded: chain K residue 517 VAL Chi-restraints excluded: chain K residue 524 HIS Chi-restraints excluded: chain K residue 534 ASP Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 663 CYS Chi-restraints excluded: chain K residue 675 CYS Chi-restraints excluded: chain K residue 700 GLU Chi-restraints excluded: chain K residue 846 CYS Chi-restraints excluded: chain K residue 890 PHE Chi-restraints excluded: chain K residue 918 SER Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1018 LEU Chi-restraints excluded: chain K residue 1055 ASN Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 248 SER Chi-restraints excluded: chain M residue 252 LYS Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 358 SER Chi-restraints excluded: chain M residue 360 ASP Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 418 PHE Chi-restraints excluded: chain M residue 452 GLN Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 533 LEU Chi-restraints excluded: chain M residue 534 ASP Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 624 SER Chi-restraints excluded: chain M residue 663 CYS Chi-restraints excluded: chain M residue 674 THR Chi-restraints excluded: chain M residue 675 CYS Chi-restraints excluded: chain M residue 700 GLU Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 846 CYS Chi-restraints excluded: chain M residue 940 VAL Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1220 LEU Chi-restraints excluded: chain M residue 1224 HIS Chi-restraints excluded: chain M residue 1229 PHE Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 85 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 698 optimal weight: 9.9990 chunk 476 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 624 optimal weight: 2.9990 chunk 346 optimal weight: 40.0000 chunk 715 optimal weight: 30.0000 chunk 579 optimal weight: 30.0000 chunk 0 optimal weight: 8.9990 chunk 428 optimal weight: 0.7980 chunk 753 optimal weight: 3.9990 chunk 211 optimal weight: 40.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 HIS C 449 ASN C 562 ASN C 701 GLN C 703 ASN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1176 HIS ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 543 ASN E 562 ASN ** E 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 881 HIS ** E1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1237 ASN ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 HIS G 235 HIS G 449 ASN ** G 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 904 GLN ** G1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 HIS I 449 ASN ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 737 ASN ** I 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 438 HIS M 449 ASN ** M 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1121 HIS ** M1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5410 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 71806 Z= 0.354 Angle : 0.728 12.999 97216 Z= 0.369 Chirality : 0.044 0.293 10731 Planarity : 0.004 0.069 12306 Dihedral : 9.431 131.561 9713 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.05 % Favored : 91.19 % Rotamer: Outliers : 6.43 % Allowed : 19.51 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.09), residues: 8708 helix: 0.18 (0.11), residues: 2324 sheet: -1.92 (0.11), residues: 1659 loop : -1.34 (0.09), residues: 4725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M1179 HIS 0.008 0.001 HIS I1176 PHE 0.025 0.002 PHE K 505 TYR 0.043 0.002 TYR H 97 ARG 0.007 0.001 ARG G 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 501 poor density : 746 time to evaluate : 5.945 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: A 146 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6773 (mm-30) REVERT: A 173 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8098 (tp) REVERT: A 267 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8442 (ttpp) REVERT: A 298 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8931 (t80) REVERT: A 504 MET cc_start: 0.5443 (mmm) cc_final: 0.5062 (mmm) REVERT: B 65 MET cc_start: 0.3964 (tpt) cc_final: 0.3626 (tpt) REVERT: C 129 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8534 (mtt180) REVERT: C 173 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7974 (tp) REVERT: C 267 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8416 (ttpp) REVERT: C 298 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8799 (t80) REVERT: C 439 ASP cc_start: 0.4594 (t0) cc_final: 0.4358 (t0) REVERT: C 454 GLN cc_start: 0.6241 (OUTLIER) cc_final: 0.5084 (tt0) REVERT: C 548 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6564 (mm) REVERT: C 1198 TYR cc_start: 0.4501 (p90) cc_final: 0.4240 (p90) REVERT: D 82 PHE cc_start: 0.1084 (t80) cc_final: 0.0600 (t80) REVERT: E 173 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7874 (tp) REVERT: E 298 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8780 (t80) REVERT: E 332 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7962 (ttp-110) REVERT: E 333 ASP cc_start: 0.6881 (m-30) cc_final: 0.6637 (m-30) REVERT: E 454 GLN cc_start: 0.5925 (OUTLIER) cc_final: 0.4785 (tt0) REVERT: E 491 MET cc_start: 0.6668 (pmm) cc_final: 0.6408 (pmm) REVERT: F 65 MET cc_start: 0.4125 (tpt) cc_final: 0.3890 (mmt) REVERT: G 173 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8312 (tp) REVERT: G 214 GLN cc_start: 0.6518 (pm20) cc_final: 0.6066 (pm20) REVERT: G 326 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8338 (mp) REVERT: G 503 LEU cc_start: 0.6421 (tp) cc_final: 0.6192 (tt) REVERT: G 925 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.5203 (mp0) REVERT: G 1238 LEU cc_start: 0.4296 (OUTLIER) cc_final: 0.3993 (mt) REVERT: I 267 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8290 (ttpt) REVERT: K 140 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8677 (tt) REVERT: K 160 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8507 (ttmt) REVERT: K 173 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8095 (tp) REVERT: K 261 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9318 (pp) REVERT: K 412 GLU cc_start: 0.7449 (tt0) cc_final: 0.7136 (tt0) REVERT: K 439 ASP cc_start: 0.4730 (t0) cc_final: 0.4319 (t0) REVERT: K 496 MET cc_start: 0.5012 (ptm) cc_final: 0.4729 (ptp) REVERT: L 65 MET cc_start: 0.5789 (tmm) cc_final: 0.4860 (tpt) REVERT: M 1202 TRP cc_start: 0.4407 (m-90) cc_final: 0.4108 (m-90) outliers start: 501 outliers final: 334 residues processed: 1150 average time/residue: 0.6045 time to fit residues: 1229.3895 Evaluate side-chains 1018 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 662 time to evaluate : 5.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 916 LYS Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 418 PHE Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 803 CYS Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 918 SER Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1055 ASN Chi-restraints excluded: chain C residue 1153 ILE Chi-restraints excluded: chain C residue 1211 GLN Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 298 PHE Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 418 PHE Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 663 CYS Chi-restraints excluded: chain E residue 712 HIS Chi-restraints excluded: chain E residue 803 CYS Chi-restraints excluded: chain E residue 846 CYS Chi-restraints excluded: chain E residue 940 VAL Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1055 ASN Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1220 LEU Chi-restraints excluded: chain E residue 1224 HIS Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1236 ASP Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 401 CYS Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 418 PHE Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 507 LEU Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 576 VAL Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 616 ASP Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 663 CYS Chi-restraints excluded: chain G residue 846 CYS Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 925 GLU Chi-restraints excluded: chain G residue 940 VAL Chi-restraints excluded: chain G residue 1007 TRP Chi-restraints excluded: chain G residue 1055 ASN Chi-restraints excluded: chain G residue 1069 VAL Chi-restraints excluded: chain G residue 1211 GLN Chi-restraints excluded: chain G residue 1224 HIS Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain G residue 1238 LEU Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1248 GLU Chi-restraints excluded: chain H residue 14 CYS Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 244 ASP Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 260 ILE Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain I residue 265 ARG Chi-restraints excluded: chain I residue 267 LYS Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 298 PHE Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 330 LEU Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain I residue 370 ILE Chi-restraints excluded: chain I residue 385 ASP Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 418 PHE Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 630 ILE Chi-restraints excluded: chain I residue 663 CYS Chi-restraints excluded: chain I residue 675 CYS Chi-restraints excluded: chain I residue 803 CYS Chi-restraints excluded: chain I residue 846 CYS Chi-restraints excluded: chain I residue 882 LEU Chi-restraints excluded: chain I residue 918 SER Chi-restraints excluded: chain I residue 999 ARG Chi-restraints excluded: chain I residue 1007 TRP Chi-restraints excluded: chain I residue 1212 THR Chi-restraints excluded: chain I residue 1214 TYR Chi-restraints excluded: chain I residue 1234 THR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 206 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 256 SER Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 264 THR Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 360 ASP Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 418 PHE Chi-restraints excluded: chain K residue 445 LEU Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 504 MET Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 517 VAL Chi-restraints excluded: chain K residue 534 ASP Chi-restraints excluded: chain K residue 576 VAL Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 630 ILE Chi-restraints excluded: chain K residue 663 CYS Chi-restraints excluded: chain K residue 803 CYS Chi-restraints excluded: chain K residue 846 CYS Chi-restraints excluded: chain K residue 918 SER Chi-restraints excluded: chain K residue 925 GLU Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1018 LEU Chi-restraints excluded: chain K residue 1069 VAL Chi-restraints excluded: chain K residue 1212 THR Chi-restraints excluded: chain K residue 1220 LEU Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain L residue 14 CYS Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 248 SER Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 313 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 360 ASP Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 418 PHE Chi-restraints excluded: chain M residue 452 GLN Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 508 ASP Chi-restraints excluded: chain M residue 517 VAL Chi-restraints excluded: chain M residue 533 LEU Chi-restraints excluded: chain M residue 534 ASP Chi-restraints excluded: chain M residue 566 LEU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 624 SER Chi-restraints excluded: chain M residue 630 ILE Chi-restraints excluded: chain M residue 663 CYS Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 846 CYS Chi-restraints excluded: chain M residue 940 VAL Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1153 ILE Chi-restraints excluded: chain M residue 1212 THR Chi-restraints excluded: chain M residue 1220 LEU Chi-restraints excluded: chain M residue 1224 HIS Chi-restraints excluded: chain M residue 1229 PHE Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 14 CYS Chi-restraints excluded: chain N residue 35 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 282 optimal weight: 4.9990 chunk 755 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 492 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 839 optimal weight: 40.0000 chunk 697 optimal weight: 7.9990 chunk 388 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 440 optimal weight: 0.0470 overall best weight: 1.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 200 GLN ** C 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 GLN E 562 ASN E 565 GLN ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 881 HIS ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 GLN K 454 GLN K 640 GLN ** K 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1176 HIS ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 737 ASN ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5328 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 71806 Z= 0.207 Angle : 0.661 13.196 97216 Z= 0.329 Chirality : 0.041 0.222 10731 Planarity : 0.004 0.063 12306 Dihedral : 8.827 112.244 9676 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.78 % Allowed : 7.22 % Favored : 92.00 % Rotamer: Outliers : 4.74 % Allowed : 21.43 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.09), residues: 8708 helix: 0.36 (0.11), residues: 2345 sheet: -1.74 (0.11), residues: 1715 loop : -1.36 (0.09), residues: 4648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 728 HIS 0.007 0.001 HIS C1176 PHE 0.031 0.001 PHE G 547 TYR 0.046 0.002 TYR D 97 ARG 0.008 0.000 ARG G 999 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 369 poor density : 762 time to evaluate : 5.896 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: A 267 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8271 (ttpp) REVERT: A 439 ASP cc_start: 0.4654 (t0) cc_final: 0.4227 (t0) REVERT: C 267 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8300 (ttpt) REVERT: C 298 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8705 (t80) REVERT: C 454 GLN cc_start: 0.5946 (OUTLIER) cc_final: 0.4748 (tt0) REVERT: D 65 MET cc_start: 0.1722 (tpt) cc_final: 0.1064 (tpt) REVERT: D 82 PHE cc_start: 0.1049 (t80) cc_final: 0.0718 (t80) REVERT: E 491 MET cc_start: 0.6495 (pmm) cc_final: 0.6271 (pmm) REVERT: F 65 MET cc_start: 0.4314 (tpt) cc_final: 0.4078 (mmt) REVERT: G 143 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.8004 (pp) REVERT: G 214 GLN cc_start: 0.6233 (pm20) cc_final: 0.5899 (pm20) REVERT: G 503 LEU cc_start: 0.6470 (tp) cc_final: 0.6264 (tt) REVERT: G 848 PHE cc_start: 0.4227 (t80) cc_final: 0.3962 (t80) REVERT: G 925 GLU cc_start: 0.5485 (OUTLIER) cc_final: 0.5057 (mp0) REVERT: H 4 GLU cc_start: 0.6506 (tp30) cc_final: 0.6260 (tp30) REVERT: H 65 MET cc_start: 0.3801 (tpt) cc_final: 0.3411 (mmt) REVERT: I 144 LYS cc_start: 0.6309 (OUTLIER) cc_final: 0.5513 (ptpp) REVERT: I 504 MET cc_start: 0.6117 (tpp) cc_final: 0.5529 (mmm) REVERT: K 126 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6098 (p90) REVERT: K 439 ASP cc_start: 0.4614 (t0) cc_final: 0.4259 (t0) REVERT: L 65 MET cc_start: 0.4993 (tmm) cc_final: 0.4345 (tpt) REVERT: L 80 MET cc_start: 0.2411 (tpt) cc_final: 0.1831 (tpt) REVERT: M 126 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.5977 (p90) REVERT: M 443 ASP cc_start: 0.5725 (t0) cc_final: 0.5460 (t0) REVERT: M 687 MET cc_start: 0.5494 (tpp) cc_final: 0.5021 (tpp) outliers start: 369 outliers final: 270 residues processed: 1051 average time/residue: 0.5991 time to fit residues: 1118.7334 Evaluate side-chains 963 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 684 time to evaluate : 5.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1055 ASN Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 418 PHE Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 803 CYS Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 918 SER Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1055 ASN Chi-restraints excluded: chain C residue 1211 GLN Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 298 PHE Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 418 PHE Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 524 HIS Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 623 PHE Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 663 CYS Chi-restraints excluded: chain E residue 712 HIS Chi-restraints excluded: chain E residue 714 LEU Chi-restraints excluded: chain E residue 803 CYS Chi-restraints excluded: chain E residue 846 CYS Chi-restraints excluded: chain E residue 940 VAL Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1055 ASN Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1224 HIS Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1236 ASP Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 418 PHE Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 616 ASP Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 663 CYS Chi-restraints excluded: chain G residue 846 CYS Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 925 GLU Chi-restraints excluded: chain G residue 940 VAL Chi-restraints excluded: chain G residue 1007 TRP Chi-restraints excluded: chain G residue 1069 VAL Chi-restraints excluded: chain G residue 1212 THR Chi-restraints excluded: chain G residue 1220 LEU Chi-restraints excluded: chain G residue 1224 HIS Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain H residue 14 CYS Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain I residue 265 ARG Chi-restraints excluded: chain I residue 274 MET Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain I residue 365 ASP Chi-restraints excluded: chain I residue 385 ASP Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 418 PHE Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 630 ILE Chi-restraints excluded: chain I residue 663 CYS Chi-restraints excluded: chain I residue 675 CYS Chi-restraints excluded: chain I residue 714 LEU Chi-restraints excluded: chain I residue 803 CYS Chi-restraints excluded: chain I residue 846 CYS Chi-restraints excluded: chain I residue 882 LEU Chi-restraints excluded: chain I residue 918 SER Chi-restraints excluded: chain I residue 1007 TRP Chi-restraints excluded: chain I residue 1069 VAL Chi-restraints excluded: chain I residue 1212 THR Chi-restraints excluded: chain I residue 1214 TYR Chi-restraints excluded: chain I residue 1234 THR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 256 SER Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 264 THR Chi-restraints excluded: chain K residue 274 MET Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 360 ASP Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 418 PHE Chi-restraints excluded: chain K residue 445 LEU Chi-restraints excluded: chain K residue 454 GLN Chi-restraints excluded: chain K residue 461 ILE Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 504 MET Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 534 ASP Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 630 ILE Chi-restraints excluded: chain K residue 663 CYS Chi-restraints excluded: chain K residue 675 CYS Chi-restraints excluded: chain K residue 803 CYS Chi-restraints excluded: chain K residue 846 CYS Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1212 THR Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 248 SER Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 305 ASP Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 360 ASP Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 418 PHE Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 534 ASP Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 624 SER Chi-restraints excluded: chain M residue 663 CYS Chi-restraints excluded: chain M residue 675 CYS Chi-restraints excluded: chain M residue 688 THR Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 846 CYS Chi-restraints excluded: chain M residue 925 GLU Chi-restraints excluded: chain M residue 934 GLU Chi-restraints excluded: chain M residue 940 VAL Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1153 ILE Chi-restraints excluded: chain M residue 1212 THR Chi-restraints excluded: chain M residue 1220 LEU Chi-restraints excluded: chain M residue 1224 HIS Chi-restraints excluded: chain M residue 1229 PHE Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 14 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 809 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 478 optimal weight: 0.0970 chunk 613 optimal weight: 5.9990 chunk 475 optimal weight: 9.9990 chunk 706 optimal weight: 2.9990 chunk 468 optimal weight: 30.0000 chunk 836 optimal weight: 30.0000 chunk 523 optimal weight: 4.9990 chunk 510 optimal weight: 0.7980 chunk 386 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN ** C 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN ** E 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 844 GLN ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 GLN G 640 GLN ** G 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 GLN I 562 ASN ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5312 moved from start: 0.6765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 71806 Z= 0.185 Angle : 0.649 11.151 97216 Z= 0.323 Chirality : 0.041 0.209 10731 Planarity : 0.004 0.077 12306 Dihedral : 8.391 100.802 9635 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.48 % Favored : 91.72 % Rotamer: Outliers : 4.51 % Allowed : 21.88 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.09), residues: 8708 helix: 0.38 (0.11), residues: 2352 sheet: -1.60 (0.11), residues: 1862 loop : -1.35 (0.09), residues: 4494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K1201 HIS 0.016 0.001 HIS K 881 PHE 0.045 0.001 PHE C 526 TYR 0.035 0.001 TYR D 97 ARG 0.005 0.000 ARG G 999 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 351 poor density : 742 time to evaluate : 6.014 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: A 267 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8187 (ttpp) REVERT: A 330 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8939 (mp) REVERT: A 418 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8673 (m-80) REVERT: A 439 ASP cc_start: 0.4694 (t0) cc_final: 0.4423 (t0) REVERT: A 761 CYS cc_start: 0.0086 (OUTLIER) cc_final: -0.0520 (t) REVERT: B 65 MET cc_start: 0.3693 (tpt) cc_final: 0.3419 (tpt) REVERT: C 267 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8243 (ttpt) REVERT: C 298 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8678 (t80) REVERT: C 454 GLN cc_start: 0.5867 (OUTLIER) cc_final: 0.4738 (tt0) REVERT: C 506 SER cc_start: 0.7179 (OUTLIER) cc_final: 0.6819 (p) REVERT: C 797 MET cc_start: 0.2775 (mmp) cc_final: 0.1813 (mmp) REVERT: C 814 MET cc_start: 0.1739 (mmm) cc_final: 0.1509 (mmm) REVERT: D 82 PHE cc_start: 0.0676 (t80) cc_final: 0.0346 (t80) REVERT: G 126 PHE cc_start: 0.6869 (OUTLIER) cc_final: 0.5873 (p90) REVERT: G 925 GLU cc_start: 0.5430 (OUTLIER) cc_final: 0.5196 (mp0) REVERT: H 65 MET cc_start: 0.3862 (tpt) cc_final: 0.3485 (mmt) REVERT: I 330 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9012 (mp) REVERT: I 761 CYS cc_start: -0.1254 (OUTLIER) cc_final: -0.2324 (t) REVERT: K 126 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.6113 (p90) REVERT: K 439 ASP cc_start: 0.4563 (t0) cc_final: 0.4228 (t0) REVERT: L 80 MET cc_start: 0.3006 (tpt) cc_final: 0.2745 (tpt) REVERT: M 126 PHE cc_start: 0.7162 (OUTLIER) cc_final: 0.5992 (p90) REVERT: M 443 ASP cc_start: 0.5674 (t0) cc_final: 0.5410 (t0) REVERT: M 687 MET cc_start: 0.5248 (tpp) cc_final: 0.4740 (tpp) outliers start: 351 outliers final: 270 residues processed: 1009 average time/residue: 0.6111 time to fit residues: 1095.2466 Evaluate side-chains 963 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 679 time to evaluate : 5.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1055 ASN Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 418 PHE Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 803 CYS Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 918 SER Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1211 GLN Chi-restraints excluded: chain C residue 1214 TYR Chi-restraints excluded: chain C residue 1224 HIS Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 298 PHE Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 418 PHE Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 623 PHE Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 712 HIS Chi-restraints excluded: chain E residue 803 CYS Chi-restraints excluded: chain E residue 846 CYS Chi-restraints excluded: chain E residue 940 VAL Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1055 ASN Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1224 HIS Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 418 PHE Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 616 ASP Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 652 GLU Chi-restraints excluded: chain G residue 663 CYS Chi-restraints excluded: chain G residue 712 HIS Chi-restraints excluded: chain G residue 846 CYS Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 925 GLU Chi-restraints excluded: chain G residue 940 VAL Chi-restraints excluded: chain G residue 1007 TRP Chi-restraints excluded: chain G residue 1069 VAL Chi-restraints excluded: chain G residue 1211 GLN Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain H residue 14 CYS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain I residue 265 ARG Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 298 PHE Chi-restraints excluded: chain I residue 330 LEU Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain I residue 365 ASP Chi-restraints excluded: chain I residue 385 ASP Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 418 PHE Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 630 ILE Chi-restraints excluded: chain I residue 663 CYS Chi-restraints excluded: chain I residue 675 CYS Chi-restraints excluded: chain I residue 761 CYS Chi-restraints excluded: chain I residue 803 CYS Chi-restraints excluded: chain I residue 846 CYS Chi-restraints excluded: chain I residue 882 LEU Chi-restraints excluded: chain I residue 918 SER Chi-restraints excluded: chain I residue 1069 VAL Chi-restraints excluded: chain I residue 1212 THR Chi-restraints excluded: chain I residue 1214 TYR Chi-restraints excluded: chain I residue 1234 THR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 206 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 256 SER Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 264 THR Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 360 ASP Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 374 MET Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 418 PHE Chi-restraints excluded: chain K residue 445 LEU Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 504 MET Chi-restraints excluded: chain K residue 534 ASP Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 630 ILE Chi-restraints excluded: chain K residue 663 CYS Chi-restraints excluded: chain K residue 675 CYS Chi-restraints excluded: chain K residue 803 CYS Chi-restraints excluded: chain K residue 846 CYS Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1069 VAL Chi-restraints excluded: chain K residue 1212 THR Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain L residue 14 CYS Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 270 THR Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 305 ASP Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 418 PHE Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 508 ASP Chi-restraints excluded: chain M residue 534 ASP Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 624 SER Chi-restraints excluded: chain M residue 663 CYS Chi-restraints excluded: chain M residue 675 CYS Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 846 CYS Chi-restraints excluded: chain M residue 940 VAL Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1212 THR Chi-restraints excluded: chain M residue 1220 LEU Chi-restraints excluded: chain M residue 1224 HIS Chi-restraints excluded: chain M residue 1240 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 517 optimal weight: 0.7980 chunk 334 optimal weight: 40.0000 chunk 499 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 164 optimal weight: 0.0870 chunk 162 optimal weight: 1.9990 chunk 531 optimal weight: 0.9990 chunk 569 optimal weight: 5.9990 chunk 413 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 657 optimal weight: 0.3980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 HIS ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1126 HIS ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1010 GLN ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 HIS I 565 GLN ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1126 HIS ** I1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 HIS K 545 GLN ** K 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 183 HIS ** M1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5271 moved from start: 0.6981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 71806 Z= 0.164 Angle : 0.651 14.446 97216 Z= 0.320 Chirality : 0.041 0.245 10731 Planarity : 0.003 0.067 12306 Dihedral : 8.155 84.922 9622 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.15 % Favored : 92.02 % Rotamer: Outliers : 4.09 % Allowed : 22.63 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.09), residues: 8708 helix: 0.38 (0.11), residues: 2352 sheet: -1.51 (0.11), residues: 1897 loop : -1.36 (0.09), residues: 4459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I1201 HIS 0.010 0.001 HIS E 881 PHE 0.040 0.001 PHE G 547 TYR 0.029 0.001 TYR D 97 ARG 0.006 0.000 ARG E 999 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 748 time to evaluate : 5.914 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: A 146 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6807 (mm-30) REVERT: A 330 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8994 (mp) REVERT: A 439 ASP cc_start: 0.4581 (t0) cc_final: 0.4152 (t0) REVERT: A 739 MET cc_start: 0.3214 (pmm) cc_final: 0.1515 (ptm) REVERT: A 761 CYS cc_start: -0.0100 (OUTLIER) cc_final: -0.0731 (t) REVERT: B 33 HIS cc_start: 0.4567 (t70) cc_final: 0.4262 (t-170) REVERT: B 65 MET cc_start: 0.3710 (tpt) cc_final: 0.3428 (tpt) REVERT: C 267 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8170 (ttpt) REVERT: C 298 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8633 (t80) REVERT: C 406 MET cc_start: 0.6287 (ptm) cc_final: 0.5881 (ttp) REVERT: C 797 MET cc_start: 0.2242 (mmp) cc_final: 0.1316 (mmp) REVERT: E 330 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8785 (mp) REVERT: G 126 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.5704 (p90) REVERT: G 761 CYS cc_start: -0.0231 (OUTLIER) cc_final: -0.1349 (t) REVERT: G 925 GLU cc_start: 0.5674 (OUTLIER) cc_final: 0.5415 (mp0) REVERT: H 65 MET cc_start: 0.3667 (tpt) cc_final: 0.3276 (mmt) REVERT: I 144 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.4875 (ptpp) REVERT: I 439 ASP cc_start: 0.4496 (t0) cc_final: 0.4157 (t0) REVERT: K 126 PHE cc_start: 0.6840 (OUTLIER) cc_final: 0.6046 (p90) REVERT: K 439 ASP cc_start: 0.4570 (t0) cc_final: 0.4104 (t0) REVERT: K 761 CYS cc_start: 0.0216 (OUTLIER) cc_final: -0.0481 (t) REVERT: M 126 PHE cc_start: 0.6990 (OUTLIER) cc_final: 0.5919 (p90) REVERT: M 443 ASP cc_start: 0.5672 (t0) cc_final: 0.5400 (t0) REVERT: M 687 MET cc_start: 0.5277 (tpp) cc_final: 0.4794 (tpp) REVERT: M 739 MET cc_start: 0.3414 (pmm) cc_final: 0.1376 (ptp) REVERT: M 848 PHE cc_start: 0.3777 (t80) cc_final: 0.3399 (t80) outliers start: 319 outliers final: 237 residues processed: 985 average time/residue: 0.6117 time to fit residues: 1074.9758 Evaluate side-chains 939 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 690 time to evaluate : 5.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 418 PHE Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 803 CYS Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 918 SER Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1199 ILE Chi-restraints excluded: chain C residue 1214 TYR Chi-restraints excluded: chain C residue 1224 HIS Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 298 PHE Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 418 PHE Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 712 HIS Chi-restraints excluded: chain E residue 940 VAL Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1224 HIS Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1236 ASP Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 418 PHE Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 616 ASP Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 663 CYS Chi-restraints excluded: chain G residue 712 HIS Chi-restraints excluded: chain G residue 761 CYS Chi-restraints excluded: chain G residue 846 CYS Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 925 GLU Chi-restraints excluded: chain G residue 940 VAL Chi-restraints excluded: chain G residue 1007 TRP Chi-restraints excluded: chain G residue 1069 VAL Chi-restraints excluded: chain G residue 1211 GLN Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain H residue 14 CYS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain I residue 265 ARG Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 305 ASP Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain I residue 365 ASP Chi-restraints excluded: chain I residue 370 ILE Chi-restraints excluded: chain I residue 385 ASP Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 418 PHE Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 491 MET Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 663 CYS Chi-restraints excluded: chain I residue 675 CYS Chi-restraints excluded: chain I residue 803 CYS Chi-restraints excluded: chain I residue 846 CYS Chi-restraints excluded: chain I residue 999 ARG Chi-restraints excluded: chain I residue 1069 VAL Chi-restraints excluded: chain I residue 1212 THR Chi-restraints excluded: chain I residue 1214 TYR Chi-restraints excluded: chain I residue 1234 THR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 256 SER Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 264 THR Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 418 PHE Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 534 ASP Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 663 CYS Chi-restraints excluded: chain K residue 675 CYS Chi-restraints excluded: chain K residue 761 CYS Chi-restraints excluded: chain K residue 803 CYS Chi-restraints excluded: chain K residue 846 CYS Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1069 VAL Chi-restraints excluded: chain K residue 1212 THR Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain L residue 14 CYS Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 270 THR Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 305 ASP Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 418 PHE Chi-restraints excluded: chain M residue 452 GLN Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 491 MET Chi-restraints excluded: chain M residue 508 ASP Chi-restraints excluded: chain M residue 534 ASP Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 624 SER Chi-restraints excluded: chain M residue 663 CYS Chi-restraints excluded: chain M residue 675 CYS Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 846 CYS Chi-restraints excluded: chain M residue 940 VAL Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1055 ASN Chi-restraints excluded: chain M residue 1224 HIS Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 35 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 761 optimal weight: 0.4980 chunk 801 optimal weight: 2.9990 chunk 731 optimal weight: 20.0000 chunk 779 optimal weight: 1.9990 chunk 469 optimal weight: 20.0000 chunk 339 optimal weight: 30.0000 chunk 612 optimal weight: 40.0000 chunk 239 optimal weight: 40.0000 chunk 704 optimal weight: 0.7980 chunk 737 optimal weight: 0.5980 chunk 776 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 562 ASN ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 HIS C 701 GLN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 844 GLN ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 449 ASN K 844 GLN ** K 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 693 HIS ** M 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5285 moved from start: 0.7146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 71806 Z= 0.174 Angle : 0.654 13.198 97216 Z= 0.319 Chirality : 0.041 0.390 10731 Planarity : 0.003 0.066 12306 Dihedral : 7.920 85.495 9603 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.21 % Favored : 91.97 % Rotamer: Outliers : 3.54 % Allowed : 23.21 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.09), residues: 8708 helix: 0.38 (0.11), residues: 2352 sheet: -1.47 (0.11), residues: 1904 loop : -1.37 (0.09), residues: 4452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 770 HIS 0.011 0.001 HIS E 881 PHE 0.037 0.001 PHE K 547 TYR 0.041 0.001 TYR A1198 ARG 0.005 0.000 ARG I 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 703 time to evaluate : 6.035 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: A 298 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8664 (t80) REVERT: A 330 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8998 (mp) REVERT: A 439 ASP cc_start: 0.4595 (t0) cc_final: 0.4152 (t0) REVERT: A 623 PHE cc_start: 0.6260 (OUTLIER) cc_final: 0.5847 (m-80) REVERT: A 739 MET cc_start: 0.3104 (pmm) cc_final: 0.1520 (ptm) REVERT: A 761 CYS cc_start: -0.0121 (OUTLIER) cc_final: -0.0741 (t) REVERT: B 65 MET cc_start: 0.3729 (tpt) cc_final: 0.3455 (tpt) REVERT: C 267 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8211 (ttpt) REVERT: C 298 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8621 (t80) REVERT: C 406 MET cc_start: 0.6291 (ptm) cc_final: 0.5856 (ttp) REVERT: C 739 MET cc_start: 0.2356 (pmm) cc_final: 0.0220 (ptm) REVERT: C 761 CYS cc_start: -0.1611 (OUTLIER) cc_final: -0.2021 (t) REVERT: C 797 MET cc_start: 0.2171 (mmp) cc_final: 0.1322 (mmp) REVERT: E 330 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8803 (mp) REVERT: G 761 CYS cc_start: 0.0050 (OUTLIER) cc_final: -0.1134 (t) REVERT: G 925 GLU cc_start: 0.5785 (OUTLIER) cc_final: 0.5502 (mp0) REVERT: H 65 MET cc_start: 0.3795 (tpt) cc_final: 0.3392 (mmt) REVERT: I 144 LYS cc_start: 0.5730 (OUTLIER) cc_final: 0.4683 (ptpp) REVERT: K 126 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6139 (p90) REVERT: K 439 ASP cc_start: 0.4445 (t0) cc_final: 0.4102 (t0) REVERT: M 443 ASP cc_start: 0.5673 (t0) cc_final: 0.5414 (t0) REVERT: M 739 MET cc_start: 0.3308 (pmm) cc_final: 0.1366 (ptp) outliers start: 276 outliers final: 241 residues processed: 915 average time/residue: 0.6084 time to fit residues: 990.7845 Evaluate side-chains 923 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 670 time to evaluate : 5.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 418 PHE Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 761 CYS Chi-restraints excluded: chain C residue 803 CYS Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 918 SER Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1224 HIS Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 418 PHE Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 623 PHE Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 663 CYS Chi-restraints excluded: chain E residue 712 HIS Chi-restraints excluded: chain E residue 940 VAL Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1220 LEU Chi-restraints excluded: chain E residue 1224 HIS Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 418 PHE Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 579 GLN Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 616 ASP Chi-restraints excluded: chain G residue 652 GLU Chi-restraints excluded: chain G residue 663 CYS Chi-restraints excluded: chain G residue 712 HIS Chi-restraints excluded: chain G residue 761 CYS Chi-restraints excluded: chain G residue 846 CYS Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 925 GLU Chi-restraints excluded: chain G residue 940 VAL Chi-restraints excluded: chain G residue 1007 TRP Chi-restraints excluded: chain G residue 1018 LEU Chi-restraints excluded: chain G residue 1069 VAL Chi-restraints excluded: chain G residue 1211 GLN Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain H residue 14 CYS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain I residue 265 ARG Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 298 PHE Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain I residue 365 ASP Chi-restraints excluded: chain I residue 370 ILE Chi-restraints excluded: chain I residue 385 ASP Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 418 PHE Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 491 MET Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 663 CYS Chi-restraints excluded: chain I residue 675 CYS Chi-restraints excluded: chain I residue 999 ARG Chi-restraints excluded: chain I residue 1069 VAL Chi-restraints excluded: chain I residue 1212 THR Chi-restraints excluded: chain I residue 1214 TYR Chi-restraints excluded: chain I residue 1234 THR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 256 SER Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 264 THR Chi-restraints excluded: chain K residue 274 MET Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 305 ASP Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 360 ASP Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 418 PHE Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 534 ASP Chi-restraints excluded: chain K residue 577 TYR Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 663 CYS Chi-restraints excluded: chain K residue 675 CYS Chi-restraints excluded: chain K residue 803 CYS Chi-restraints excluded: chain K residue 846 CYS Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1069 VAL Chi-restraints excluded: chain K residue 1212 THR Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain L residue 14 CYS Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 270 THR Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 305 ASP Chi-restraints excluded: chain M residue 313 ILE Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 418 PHE Chi-restraints excluded: chain M residue 452 GLN Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 508 ASP Chi-restraints excluded: chain M residue 534 ASP Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 624 SER Chi-restraints excluded: chain M residue 663 CYS Chi-restraints excluded: chain M residue 675 CYS Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 846 CYS Chi-restraints excluded: chain M residue 940 VAL Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1055 ASN Chi-restraints excluded: chain M residue 1224 HIS Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 35 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 511 optimal weight: 0.0370 chunk 824 optimal weight: 0.9980 chunk 503 optimal weight: 0.6980 chunk 391 optimal weight: 2.9990 chunk 573 optimal weight: 7.9990 chunk 864 optimal weight: 0.9980 chunk 795 optimal weight: 10.0000 chunk 688 optimal weight: 0.0010 chunk 71 optimal weight: 10.0000 chunk 531 optimal weight: 1.9990 chunk 422 optimal weight: 0.9980 overall best weight: 0.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS ** E 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1126 HIS ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 137 GLN M 153 HIS M 881 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5255 moved from start: 0.7287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.124 71806 Z= 0.168 Angle : 0.655 13.143 97216 Z= 0.318 Chirality : 0.041 0.299 10731 Planarity : 0.003 0.067 12306 Dihedral : 7.798 84.757 9599 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.06 % Favored : 92.15 % Rotamer: Outliers : 3.08 % Allowed : 23.76 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.09), residues: 8708 helix: 0.40 (0.11), residues: 2352 sheet: -1.39 (0.11), residues: 1911 loop : -1.36 (0.09), residues: 4445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 770 HIS 0.010 0.001 HIS E 881 PHE 0.038 0.001 PHE K 547 TYR 0.032 0.001 TYR A1198 ARG 0.006 0.000 ARG E 434 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 725 time to evaluate : 5.911 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: A 298 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8612 (t80) REVERT: A 330 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8962 (mp) REVERT: A 623 PHE cc_start: 0.6166 (OUTLIER) cc_final: 0.5703 (m-80) REVERT: A 739 MET cc_start: 0.3017 (pmm) cc_final: 0.1320 (ptm) REVERT: B 65 MET cc_start: 0.3830 (tpt) cc_final: 0.3616 (tpt) REVERT: C 267 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8079 (ttpt) REVERT: C 298 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8605 (t80) REVERT: C 406 MET cc_start: 0.6104 (ptm) cc_final: 0.5718 (ttp) REVERT: C 761 CYS cc_start: -0.1534 (OUTLIER) cc_final: -0.1926 (t) REVERT: C 797 MET cc_start: 0.2140 (mmp) cc_final: 0.1316 (mmp) REVERT: E 160 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8601 (mtmm) REVERT: G 761 CYS cc_start: 0.0032 (OUTLIER) cc_final: -0.1147 (t) REVERT: H 65 MET cc_start: 0.3862 (tpt) cc_final: 0.3442 (mmt) REVERT: I 166 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.6041 (mm-30) REVERT: K 439 ASP cc_start: 0.4412 (t0) cc_final: 0.4072 (t0) REVERT: M 443 ASP cc_start: 0.5694 (t0) cc_final: 0.5406 (t0) REVERT: M 739 MET cc_start: 0.4015 (pmm) cc_final: 0.1785 (ptp) REVERT: M 848 PHE cc_start: 0.4248 (t80) cc_final: 0.3854 (t80) outliers start: 240 outliers final: 208 residues processed: 908 average time/residue: 0.5990 time to fit residues: 969.4163 Evaluate side-chains 898 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 681 time to evaluate : 5.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 418 PHE Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 761 CYS Chi-restraints excluded: chain C residue 803 CYS Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 918 SER Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1224 HIS Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 418 PHE Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 663 CYS Chi-restraints excluded: chain E residue 712 HIS Chi-restraints excluded: chain E residue 847 ASP Chi-restraints excluded: chain E residue 940 VAL Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1220 LEU Chi-restraints excluded: chain E residue 1224 HIS Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 418 PHE Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 579 GLN Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 652 GLU Chi-restraints excluded: chain G residue 663 CYS Chi-restraints excluded: chain G residue 712 HIS Chi-restraints excluded: chain G residue 761 CYS Chi-restraints excluded: chain G residue 846 CYS Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 940 VAL Chi-restraints excluded: chain G residue 1007 TRP Chi-restraints excluded: chain G residue 1018 LEU Chi-restraints excluded: chain G residue 1069 VAL Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain H residue 14 CYS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 298 PHE Chi-restraints excluded: chain I residue 305 ASP Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain I residue 365 ASP Chi-restraints excluded: chain I residue 370 ILE Chi-restraints excluded: chain I residue 385 ASP Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 418 PHE Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 491 MET Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 663 CYS Chi-restraints excluded: chain I residue 675 CYS Chi-restraints excluded: chain I residue 1069 VAL Chi-restraints excluded: chain I residue 1212 THR Chi-restraints excluded: chain I residue 1214 TYR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 256 SER Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 264 THR Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 305 ASP Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 360 ASP Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 418 PHE Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 534 ASP Chi-restraints excluded: chain K residue 577 TYR Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 663 CYS Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1069 VAL Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain L residue 14 CYS Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 270 THR Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 305 ASP Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 418 PHE Chi-restraints excluded: chain M residue 452 GLN Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 491 MET Chi-restraints excluded: chain M residue 508 ASP Chi-restraints excluded: chain M residue 534 ASP Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 663 CYS Chi-restraints excluded: chain M residue 675 CYS Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 846 CYS Chi-restraints excluded: chain M residue 940 VAL Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1193 ILE Chi-restraints excluded: chain M residue 1224 HIS Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 14 CYS Chi-restraints excluded: chain N residue 35 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 546 optimal weight: 30.0000 chunk 733 optimal weight: 0.8980 chunk 210 optimal weight: 50.0000 chunk 634 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 689 optimal weight: 2.9990 chunk 288 optimal weight: 10.0000 chunk 708 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 GLN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 449 ASN E 490 HIS ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 731 ASN ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 562 ASN ** I 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 737 ASN ** I 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 441 GLN ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 137 GLN ** M 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 562 ASN ** M1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.202995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.167220 restraints weight = 139469.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.167582 restraints weight = 225525.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.163034 restraints weight = 124052.524| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.7464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 71806 Z= 0.275 Angle : 0.695 12.089 97216 Z= 0.340 Chirality : 0.042 0.369 10731 Planarity : 0.004 0.068 12306 Dihedral : 7.886 85.091 9588 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.96 % Favored : 91.31 % Rotamer: Outliers : 3.39 % Allowed : 23.57 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.09), residues: 8708 helix: 0.29 (0.11), residues: 2338 sheet: -1.43 (0.11), residues: 1869 loop : -1.43 (0.09), residues: 4501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 770 HIS 0.017 0.001 HIS A 748 PHE 0.037 0.002 PHE K 547 TYR 0.026 0.002 TYR A1198 ARG 0.008 0.000 ARG E 434 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18971.11 seconds wall clock time: 334 minutes 27.58 seconds (20067.58 seconds total)