Starting phenix.real_space_refine on Fri Nov 17 21:54:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/11_2023/3jbt_6480_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/11_2023/3jbt_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_6480/11_2023/3jbt_6480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/11_2023/3jbt_6480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/11_2023/3jbt_6480_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/11_2023/3jbt_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: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 26.65, 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: 23.11 Conformation dependent library (CDL) restraints added in 9.4 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: 13.84 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: 34.48 Time building geometry restraints manager: 25.31 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: 38797 26.23 - 52.45: 3078 52.45 - 78.68: 853 78.68 - 104.90: 98 104.90 - 131.13: 7 Dihedral angle restraints: 42833 sinusoidal: 17430 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 42830 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: 0.010 Normalize map: mean=0, sd=1: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.990 Check model and map are aligned: 0.790 Set scattering table: 0.490 Process input model: 154.710 Find NCS groups from input model: 3.880 Set up NCS constraints: 0.600 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: 0.020 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.120 ------------------------------------------------------------------------------- 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 : 19.556 131.128 26264 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 *********************** 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 : 6.105 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 outliers start: 1421 outliers final: 385 residues processed: 2741 average time/residue: 0.7138 time to fit residues: 3273.8470 Evaluate side-chains 1353 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 385 poor density : 968 time to evaluate : 6.008 Switching outliers to nearest non-outliers outliers start: 385 outliers final: 0 residues processed: 385 average time/residue: 0.6572 time to fit residues: 446.8257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 732 optimal weight: 1.9990 chunk 657 optimal weight: 4.9990 chunk 365 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 443 optimal weight: 6.9990 chunk 351 optimal weight: 7.9990 chunk 680 optimal weight: 40.0000 chunk 263 optimal weight: 0.8980 chunk 413 optimal weight: 6.9990 chunk 506 optimal weight: 2.9990 chunk 788 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 347 ASN A 420 ASN A 457 HIS A 471 HIS A 485 ASN A 583 GLN A 709 ASN ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 457 HIS 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 ** C1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 441 GLN E 457 HIS E 471 HIS E 583 GLN ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 ASN ** E 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 933 ASN ** E1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 347 ASN G 420 ASN G 438 HIS G 457 HIS G 471 HIS G 477 GLN G 583 GLN G 709 ASN ** G 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN I 200 GLN I 201 ASN I 219 ASN I 257 GLN I 347 ASN I 420 ASN I 457 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** ** I1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN K 183 HIS K 200 GLN K 201 ASN K 257 GLN K 311 HIS K 347 ASN K 420 ASN K 441 GLN K 457 HIS K 471 HIS K 583 GLN ** K 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 709 ASN ** K 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 933 ASN ** K1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN M 137 GLN M 200 GLN M 201 ASN M 219 ASN M 347 ASN M 420 ASN M 441 GLN M 457 HIS M 471 HIS M 583 GLN M 709 ASN ** M 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 933 ASN ** M1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN Total number of N/Q/H flips: 91 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5174 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 71806 Z= 0.330 Angle : 0.855 13.677 97216 Z= 0.442 Chirality : 0.049 0.456 10731 Planarity : 0.006 0.059 12306 Dihedral : 7.881 136.413 9338 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 1.09 % Allowed : 6.87 % Favored : 92.04 % Rotamer: Outliers : 4.94 % Allowed : 17.89 % Favored : 77.17 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.05 (0.09), residues: 8708 helix: 0.55 (0.10), residues: 2282 sheet: -1.48 (0.13), residues: 1554 loop : -1.01 (0.09), residues: 4872 *********************** 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 1478 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 385 poor density : 1093 time to evaluate : 7.392 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 outliers start: 385 outliers final: 182 residues processed: 1367 average time/residue: 0.6498 time to fit residues: 1565.4315 Evaluate side-chains 959 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 777 time to evaluate : 6.036 Switching outliers to nearest non-outliers outliers start: 182 outliers final: 0 residues processed: 182 average time/residue: 0.5587 time to fit residues: 198.2952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 656 optimal weight: 0.0060 chunk 536 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 789 optimal weight: 6.9990 chunk 853 optimal weight: 3.9990 chunk 703 optimal weight: 6.9990 chunk 783 optimal weight: 6.9990 chunk 269 optimal weight: 0.7980 chunk 633 optimal weight: 2.9990 overall best weight: 2.3602 ------------------------------------------------------------------------------- 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 438 HIS A 471 HIS A 562 ASN A 565 GLN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN A 933 ASN ** A1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN C 137 GLN C 259 GLN C 477 GLN C 562 ASN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN C 933 ASN ** C1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 ASN D 42 GLN E 438 HIS E 562 ASN E 904 GLN ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN G 449 ASN G 562 ASN ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 904 GLN G 933 ASN G1176 HIS H 42 GLN I 449 ASN I 562 ASN I 904 GLN I 933 ASN I1001 GLN ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1163 HIS J 42 GLN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 471 HIS K 562 ASN K 904 GLN ** K1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1237 ASN L 42 GLN ** M 137 GLN ** 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 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 904 GLN ** M1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1237 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5262 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 71806 Z= 0.286 Angle : 0.735 10.034 97216 Z= 0.376 Chirality : 0.044 0.246 10731 Planarity : 0.004 0.064 12306 Dihedral : 7.569 147.595 9338 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.71 % Favored : 91.46 % Rotamer: Outliers : 3.31 % Allowed : 19.64 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.09), residues: 8708 helix: 0.51 (0.10), residues: 2331 sheet: -1.49 (0.12), residues: 1659 loop : -1.20 (0.09), residues: 4718 *********************** 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 1129 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 871 time to evaluate : 6.254 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 outliers start: 258 outliers final: 137 residues processed: 1061 average time/residue: 0.6262 time to fit residues: 1182.1012 Evaluate side-chains 869 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 732 time to evaluate : 6.043 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 0 residues processed: 137 average time/residue: 0.5438 time to fit residues: 146.9688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 780 optimal weight: 0.0970 chunk 593 optimal weight: 30.0000 chunk 409 optimal weight: 1.9990 chunk 87 optimal weight: 50.0000 chunk 376 optimal weight: 2.9990 chunk 530 optimal weight: 0.8980 chunk 792 optimal weight: 6.9990 chunk 839 optimal weight: 40.0000 chunk 414 optimal weight: 5.9990 chunk 751 optimal weight: 0.0470 chunk 226 optimal weight: 30.0000 overall best weight: 1.2080 ------------------------------------------------------------------------------- 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 ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN C 565 GLN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1176 HIS C1237 ASN E 562 ASN E 737 ASN E1176 HIS G 449 ASN G 562 ASN G 565 GLN ** G 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 449 ASN I 562 ASN I 565 GLN ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 565 GLN ** K 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1176 HIS K1237 ASN M 562 ASN ** M 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1055 ASN M1176 HIS M1237 ASN ** 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: 0.5231 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 71806 Z= 0.203 Angle : 0.680 11.591 97216 Z= 0.343 Chirality : 0.042 0.312 10731 Planarity : 0.004 0.065 12306 Dihedral : 7.313 142.714 9338 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.10 % Favored : 92.10 % Rotamer: Outliers : 2.49 % Allowed : 20.81 % Favored : 76.70 % 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: -1.28 (0.09), residues: 8708 helix: 0.48 (0.11), residues: 2324 sheet: -1.52 (0.12), residues: 1659 loop : -1.26 (0.09), residues: 4725 *********************** 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 1007 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 813 time to evaluate : 6.120 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 outliers start: 194 outliers final: 107 residues processed: 941 average time/residue: 0.6066 time to fit residues: 1026.0986 Evaluate side-chains 811 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 704 time to evaluate : 6.122 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 2 residues processed: 107 average time/residue: 0.5118 time to fit residues: 113.1518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 698 optimal weight: 6.9990 chunk 476 optimal weight: 30.0000 chunk 12 optimal weight: 6.9990 chunk 624 optimal weight: 2.9990 chunk 346 optimal weight: 40.0000 chunk 715 optimal weight: 30.0000 chunk 579 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 428 optimal weight: 0.0570 chunk 753 optimal weight: 1.9990 chunk 211 optimal weight: 40.0000 overall best weight: 3.8106 ------------------------------------------------------------------------------- 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 438 HIS C 449 ASN C 562 ASN C 701 GLN C 703 ASN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 881 HIS ** C1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN ** E 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN G 171 HIS G 346 GLN ** G 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 HIS I 438 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1176 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** M 438 HIS ** 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** N 42 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5421 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 71806 Z= 0.385 Angle : 0.757 14.503 97216 Z= 0.380 Chirality : 0.044 0.271 10731 Planarity : 0.004 0.068 12306 Dihedral : 7.709 168.412 9338 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.05 % Favored : 91.16 % Rotamer: Outliers : 3.22 % Allowed : 21.23 % Favored : 75.55 % 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: -1.65 (0.09), residues: 8708 helix: 0.13 (0.10), residues: 2310 sheet: -1.94 (0.11), residues: 1638 loop : -1.38 (0.09), residues: 4760 *********************** 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 1002 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 751 time to evaluate : 6.079 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 outliers start: 251 outliers final: 124 residues processed: 948 average time/residue: 0.6163 time to fit residues: 1049.5813 Evaluate side-chains 776 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 652 time to evaluate : 6.084 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 124 outliers final: 6 residues processed: 124 average time/residue: 0.5308 time to fit residues: 133.3260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 282 optimal weight: 3.9990 chunk 755 optimal weight: 0.0370 chunk 165 optimal weight: 0.9990 chunk 492 optimal weight: 2.9990 chunk 207 optimal weight: 30.0000 chunk 839 optimal weight: 10.0000 chunk 697 optimal weight: 10.0000 chunk 388 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 277 optimal weight: 0.7980 chunk 440 optimal weight: 6.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 ASN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1224 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** ** C 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 GLN ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN E 565 GLN ** 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** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 640 GLN ** 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 438 HIS ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 737 ASN ** 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 200 GLN ** K 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 545 GLN K 640 GLN ** K 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1055 ASN ** M1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5332 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 71806 Z= 0.211 Angle : 0.670 10.659 97216 Z= 0.334 Chirality : 0.041 0.223 10731 Planarity : 0.004 0.058 12306 Dihedral : 7.347 153.860 9338 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.29 % Favored : 91.89 % Rotamer: Outliers : 1.80 % Allowed : 22.67 % Favored : 75.54 % 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: -1.54 (0.09), residues: 8708 helix: 0.31 (0.11), residues: 2324 sheet: -1.75 (0.12), residues: 1624 loop : -1.42 (0.09), residues: 4760 *********************** 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 905 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 765 time to evaluate : 6.262 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 outliers start: 140 outliers final: 69 residues processed: 853 average time/residue: 0.6181 time to fit residues: 941.1814 Evaluate side-chains 745 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 676 time to evaluate : 6.064 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 7 residues processed: 69 average time/residue: 0.5298 time to fit residues: 77.7076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 809 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 478 optimal weight: 40.0000 chunk 613 optimal weight: 6.9990 chunk 475 optimal weight: 7.9990 chunk 706 optimal weight: 0.0570 chunk 468 optimal weight: 7.9990 chunk 836 optimal weight: 30.0000 chunk 523 optimal weight: 3.9990 chunk 510 optimal weight: 1.9990 chunk 386 optimal weight: 0.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 562 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS C 562 ASN ** C 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 GLN E 562 ASN ** E 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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** ** G1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 GLN ** I 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 454 GLN ** K 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 844 GLN ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 737 ASN ** M1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5338 moved from start: 0.6841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 71806 Z= 0.211 Angle : 0.663 10.966 97216 Z= 0.329 Chirality : 0.041 0.240 10731 Planarity : 0.004 0.070 12306 Dihedral : 7.231 155.504 9338 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.81 % Favored : 91.36 % Rotamer: Outliers : 1.63 % Allowed : 23.04 % Favored : 75.33 % 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: -1.54 (0.09), residues: 8708 helix: 0.33 (0.11), residues: 2331 sheet: -1.73 (0.11), residues: 1673 loop : -1.44 (0.09), residues: 4704 *********************** 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 856 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 729 time to evaluate : 6.292 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 outliers start: 127 outliers final: 60 residues processed: 824 average time/residue: 0.6331 time to fit residues: 930.8912 Evaluate side-chains 728 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 668 time to evaluate : 6.168 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 7 residues processed: 60 average time/residue: 0.5390 time to fit residues: 69.7299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 517 optimal weight: 3.9990 chunk 334 optimal weight: 0.5980 chunk 499 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 531 optimal weight: 0.0070 chunk 569 optimal weight: 5.9990 chunk 413 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 657 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A 477 GLN A 562 ASN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1224 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 881 HIS C1126 HIS ** C1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1126 HIS I1224 HIS ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 454 GLN ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 881 HIS ** M1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5278 moved from start: 0.7013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 71806 Z= 0.163 Angle : 0.655 10.744 97216 Z= 0.322 Chirality : 0.041 0.285 10731 Planarity : 0.003 0.069 12306 Dihedral : 6.929 144.839 9338 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.22 % Favored : 91.95 % Rotamer: Outliers : 1.07 % Allowed : 24.00 % Favored : 74.93 % 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: 0.37 (0.11), residues: 2331 sheet: -1.63 (0.11), residues: 1820 loop : -1.40 (0.09), residues: 4557 *********************** 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 833 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 750 time to evaluate : 6.143 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 outliers start: 83 outliers final: 40 residues processed: 806 average time/residue: 0.6263 time to fit residues: 901.4575 Evaluate side-chains 707 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 667 time to evaluate : 6.113 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 7 residues processed: 40 average time/residue: 0.5263 time to fit residues: 48.3803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 30.0000 chunk 731 optimal weight: 0.7980 chunk 779 optimal weight: 0.4980 chunk 469 optimal weight: 0.9990 chunk 339 optimal weight: 20.0000 chunk 612 optimal weight: 0.0170 chunk 239 optimal weight: 8.9990 chunk 704 optimal weight: 0.9980 chunk 737 optimal weight: 20.0000 chunk 776 optimal weight: 0.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** 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** B 33 HIS C 562 ASN C 701 GLN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 ASN ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS ** G 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN I 562 ASN ** I 614 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** ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 485 ASN ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 153 HIS M 693 HIS ** M 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5261 moved from start: 0.7163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 71806 Z= 0.165 Angle : 0.658 11.133 97216 Z= 0.322 Chirality : 0.041 0.285 10731 Planarity : 0.004 0.071 12306 Dihedral : 6.754 140.883 9338 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.15 % Favored : 92.04 % Rotamer: Outliers : 0.60 % Allowed : 24.63 % Favored : 74.77 % 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: 0.34 (0.11), residues: 2331 sheet: -1.52 (0.11), residues: 1855 loop : -1.43 (0.09), residues: 4522 *********************** 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 783 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 736 time to evaluate : 6.174 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 outliers start: 47 outliers final: 28 residues processed: 766 average time/residue: 0.6403 time to fit residues: 877.4708 Evaluate side-chains 709 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 681 time to evaluate : 6.570 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 7 residues processed: 28 average time/residue: 0.5594 time to fit residues: 38.5284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 511 optimal weight: 2.9990 chunk 824 optimal weight: 10.0000 chunk 503 optimal weight: 0.6980 chunk 391 optimal weight: 0.6980 chunk 573 optimal weight: 8.9990 chunk 864 optimal weight: 0.0070 chunk 795 optimal weight: 8.9990 chunk 688 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 531 optimal weight: 0.0170 chunk 422 optimal weight: 6.9990 overall best weight: 0.8838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** C 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 614 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 562 ASN ** I 614 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** ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 562 ASN ** M 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5273 moved from start: 0.7303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 71806 Z= 0.173 Angle : 0.661 11.523 97216 Z= 0.322 Chirality : 0.041 0.274 10731 Planarity : 0.004 0.071 12306 Dihedral : 6.619 142.276 9338 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.29 % Favored : 91.92 % Rotamer: Outliers : 0.44 % Allowed : 24.93 % Favored : 74.64 % 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: -1.45 (0.09), residues: 8708 helix: 0.37 (0.11), residues: 2331 sheet: -1.51 (0.11), residues: 1848 loop : -1.40 (0.09), residues: 4529 ********************** 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 742 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 708 time to evaluate : 7.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 22 residues processed: 727 average time/residue: 0.6274 time to fit residues: 815.3494 Evaluate side-chains 705 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 683 time to evaluate : 6.054 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 22 average time/residue: 0.5272 time to fit residues: 30.6634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 546 optimal weight: 8.9990 chunk 733 optimal weight: 6.9990 chunk 210 optimal weight: 50.0000 chunk 634 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 191 optimal weight: 30.0000 chunk 689 optimal weight: 0.9990 chunk 288 optimal weight: 3.9990 chunk 708 optimal weight: 6.9990 chunk 87 optimal weight: 50.0000 chunk 127 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** A 844 GLN ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 ASN ** C 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 844 GLN E1126 HIS ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 747 ASN ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 614 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** ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 543 ASN ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 731 ASN ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 562 ASN M 731 ASN ** M 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.204326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.168928 restraints weight = 140065.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.169279 restraints weight = 217750.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.165546 restraints weight = 121922.503| |-----------------------------------------------------------------------------| r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.7495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 71806 Z= 0.208 Angle : 0.665 11.760 97216 Z= 0.325 Chirality : 0.041 0.270 10731 Planarity : 0.004 0.071 12306 Dihedral : 6.643 156.335 9338 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.80 % Favored : 91.46 % Rotamer: Outliers : 0.55 % Allowed : 25.00 % Favored : 74.44 % 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: -1.46 (0.09), residues: 8708 helix: 0.38 (0.11), residues: 2289 sheet: -1.39 (0.11), residues: 1890 loop : -1.46 (0.09), residues: 4529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18693.53 seconds wall clock time: 329 minutes 45.71 seconds (19785.71 seconds total)