Starting phenix.real_space_refine (version: dev) on Wed Apr 6 17:03:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/04_2022/3jbt_6480_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/04_2022/3jbt_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_6480/04_2022/3jbt_6480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/04_2022/3jbt_6480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/04_2022/3jbt_6480_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/04_2022/3jbt_6480_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-dev-4553/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: {'DTP': 1, ' MG': 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: {'DTP': 1, ' MG': 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: {'DTP': 1, ' MG': 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: {'DTP': 1, ' MG': 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: {'DTP': 1, ' MG': 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: {'DTP': 1, ' MG': 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: {'DTP': 1, ' MG': 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: 28.88, per 1000 atoms: 0.41 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: 24.06 Conformation dependent library (CDL) restraints added in 7.8 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: 8.94 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: 33.62 Time building geometry restraints manager: 26.17 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.050 Extract box with map and model: 11.980 Check model and map are aligned: 0.820 Convert atoms to be neutral: 0.470 Process input model: 151.150 Find NCS groups from input model: 3.750 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4954 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 : 70.45 Ramachandran Plot: Outliers : 3.64 % Allowed : 8.02 % Favored : 88.34 % Rotamer Outliers : 18.24 % 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 : 6.239 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: 0.7244 time to fit residues: 3331.2343 Evaluate side-chains 1336 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 385 poor density : 951 time to evaluate : 6.276 Switching outliers to nearest non-outliers outliers start: 385 outliers final: 0 residues processed: 385 average time/residue: 0.6318 time to fit residues: 429.6405 ------------------------------------------------------------------------------- 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: 0.5980 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: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 201 ASN A 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** ** A1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN C 137 GLN C 200 GLN C 201 ASN C 219 ASN C 259 GLN C 347 ASN C 420 ASN C 457 HIS ** C 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** C 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 ASN ** C1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 200 GLN E 201 ASN E 219 ASN E 347 ASN E 420 ASN 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** ** 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 235 HIS G 257 GLN G 347 ASN G 420 ASN G 438 HIS G 457 HIS G 471 HIS G 477 GLN G 485 ASN 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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** ** 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: 84 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5141 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 71806 Z= 0.292 Angle : 0.843 14.590 97216 Z= 0.435 Chirality : 0.048 0.440 10731 Planarity : 0.006 0.125 12306 Dihedral : 7.809 128.032 9338 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 1.09 % Allowed : 6.75 % Favored : 92.16 % Rotamer Outliers : 4.58 % 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: -1.01 (0.09), residues: 8708 helix: 0.55 (0.10), residues: 2289 sheet: -1.39 (0.13), residues: 1645 loop : -0.97 (0.09), residues: 4774 *********************** 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 1469 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 357 poor density : 1112 time to evaluate : 7.490 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 outliers start: 357 outliers final: 170 residues processed: 1361 average time/residue: 0.6262 time to fit residues: 1493.8937 Evaluate side-chains 940 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 770 time to evaluate : 6.196 Switching outliers to nearest non-outliers outliers start: 170 outliers final: 0 residues processed: 170 average time/residue: 0.5314 time to fit residues: 177.8214 ------------------------------------------------------------------------------- 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: 40.0000 chunk 244 optimal weight: 6.9990 chunk 656 optimal weight: 0.2980 chunk 536 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 789 optimal weight: 6.9990 chunk 853 optimal weight: 1.9990 chunk 703 optimal weight: 10.0000 chunk 783 optimal weight: 9.9990 chunk 269 optimal weight: 0.9980 chunk 633 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 543 ASN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** A1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 ASN B 42 GLN C 477 GLN C 562 ASN ** C 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN C1176 HIS C1237 ASN D 42 GLN E 441 GLN E 562 ASN E 904 GLN ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN G 562 ASN ** G 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 904 GLN G1176 HIS H 42 GLN I 438 HIS I 449 ASN I 562 ASN I 904 GLN I1001 GLN ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 471 HIS K 562 ASN ** K 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 904 GLN K1176 HIS K1237 ASN ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 GLN M 471 HIS M 545 GLN ** M 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 565 GLN M 614 HIS ** M 656 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: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5166 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.101 71806 Z= 0.216 Angle : 0.719 9.539 97216 Z= 0.367 Chirality : 0.043 0.260 10731 Planarity : 0.005 0.123 12306 Dihedral : 7.285 120.861 9338 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.21 % Favored : 91.95 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.09), residues: 8708 helix: 0.57 (0.10), residues: 2324 sheet: -1.35 (0.12), residues: 1659 loop : -1.19 (0.09), residues: 4725 *********************** 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 1153 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 921 time to evaluate : 6.231 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 outliers start: 232 outliers final: 119 residues processed: 1081 average time/residue: 0.6288 time to fit residues: 1212.0171 Evaluate side-chains 870 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 751 time to evaluate : 6.271 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 0 residues processed: 119 average time/residue: 0.5310 time to fit residues: 127.0661 ------------------------------------------------------------------------------- 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: 0.7980 chunk 593 optimal weight: 30.0000 chunk 409 optimal weight: 0.0000 chunk 87 optimal weight: 50.0000 chunk 376 optimal weight: 1.9990 chunk 530 optimal weight: 4.9990 chunk 792 optimal weight: 10.0000 chunk 839 optimal weight: 40.0000 chunk 414 optimal weight: 9.9990 chunk 751 optimal weight: 0.0000 chunk 226 optimal weight: 9.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 562 ASN A 565 GLN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1176 HIS A1237 ASN C 524 HIS C 562 ASN ** C 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 HIS E 441 GLN ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1176 HIS G 565 GLN ** G 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 933 ASN I 449 ASN I 562 ASN I 737 ASN I 933 ASN ** I1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 441 GLN K 562 ASN K 565 GLN ** K 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1237 ASN L 42 GLN ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 GLN M 468 HIS ** M 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 933 ASN M1176 HIS M1237 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5229 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 71806 Z= 0.226 Angle : 0.692 11.957 97216 Z= 0.348 Chirality : 0.042 0.191 10731 Planarity : 0.004 0.127 12306 Dihedral : 7.000 129.157 9338 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.21 % Favored : 91.98 % Rotamer Outliers : 2.31 % 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: -1.18 (0.09), residues: 8708 helix: 0.54 (0.11), residues: 2331 sheet: -1.37 (0.12), residues: 1659 loop : -1.22 (0.09), residues: 4718 *********************** 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 983 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 803 time to evaluate : 6.385 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 outliers start: 180 outliers final: 98 residues processed: 922 average time/residue: 0.5982 time to fit residues: 998.4615 Evaluate side-chains 799 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 701 time to evaluate : 6.270 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 98 outliers final: 1 residues processed: 98 average time/residue: 0.5089 time to fit residues: 103.5633 ------------------------------------------------------------------------------- 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: 40.0000 chunk 476 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 624 optimal weight: 0.4980 chunk 346 optimal weight: 30.0000 chunk 715 optimal weight: 30.0000 chunk 579 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 428 optimal weight: 7.9990 chunk 753 optimal weight: 0.6980 chunk 211 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 HIS C 562 ASN C 565 GLN ** C 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 881 HIS ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 ASN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN E 562 ASN ** E 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 933 ASN ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 HIS G 693 HIS ** 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 562 ASN ** I 656 HIS ** 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 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 562 ASN ** K 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 709 ASN K 933 ASN ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 438 HIS ** M 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1055 ASN ** M1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5348 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.098 71806 Z= 0.305 Angle : 0.703 11.509 97216 Z= 0.355 Chirality : 0.043 0.216 10731 Planarity : 0.004 0.122 12306 Dihedral : 7.012 161.893 9338 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.61 % Favored : 91.57 % Rotamer Outliers : 2.44 % 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: -1.37 (0.09), residues: 8708 helix: 0.39 (0.11), residues: 2331 sheet: -1.54 (0.12), residues: 1694 loop : -1.31 (0.09), residues: 4683 *********************** 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 948 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 758 time to evaluate : 6.271 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 outliers start: 190 outliers final: 99 residues processed: 904 average time/residue: 0.6057 time to fit residues: 977.8310 Evaluate side-chains 776 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 677 time to evaluate : 6.277 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 2 residues processed: 99 average time/residue: 0.4984 time to fit residues: 103.2116 ------------------------------------------------------------------------------- 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: 0.9980 chunk 755 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 492 optimal weight: 4.9990 chunk 207 optimal weight: 40.0000 chunk 839 optimal weight: 20.0000 chunk 697 optimal weight: 0.4980 chunk 388 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 277 optimal weight: 2.9990 chunk 440 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** 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 C 703 ASN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN ** E 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 GLN I 562 ASN ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** M 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5287 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 71806 Z= 0.192 Angle : 0.655 11.321 97216 Z= 0.327 Chirality : 0.041 0.211 10731 Planarity : 0.004 0.094 12306 Dihedral : 6.697 146.181 9338 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.02 % Favored : 92.16 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.09), residues: 8708 helix: 0.49 (0.11), residues: 2345 sheet: -1.65 (0.11), residues: 1736 loop : -1.32 (0.09), residues: 4627 *********************** 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 925 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 787 time to evaluate : 6.277 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: 138 outliers final: 69 residues processed: 882 average time/residue: 0.5992 time to fit residues: 941.4408 Evaluate side-chains 769 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 700 time to evaluate : 6.254 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 4 residues processed: 69 average time/residue: 0.5118 time to fit residues: 75.6932 ------------------------------------------------------------------------------- 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: 10.0000 chunk 94 optimal weight: 9.9990 chunk 478 optimal weight: 5.9990 chunk 613 optimal weight: 20.0000 chunk 475 optimal weight: 9.9990 chunk 706 optimal weight: 0.0370 chunk 468 optimal weight: 0.2980 chunk 836 optimal weight: 30.0000 chunk 523 optimal weight: 4.9990 chunk 510 optimal weight: 1.9990 chunk 386 optimal weight: 0.8980 overall best weight: 1.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN A 562 ASN A 640 GLN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 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** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 GLN E 565 GLN ** E 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 GLN G 614 HIS ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 562 ASN ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 GLN ** K 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 ASN ** M 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 737 ASN ** M 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1055 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5320 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.122 71806 Z= 0.218 Angle : 0.660 10.864 97216 Z= 0.329 Chirality : 0.041 0.176 10731 Planarity : 0.004 0.132 12306 Dihedral : 6.599 153.586 9338 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.37 % Favored : 91.80 % Rotamer Outliers : 1.82 % 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: -1.44 (0.09), residues: 8708 helix: 0.40 (0.11), residues: 2352 sheet: -1.66 (0.12), residues: 1582 loop : -1.40 (0.09), residues: 4774 *********************** 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 892 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 750 time to evaluate : 7.495 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: 142 outliers final: 68 residues processed: 853 average time/residue: 0.6068 time to fit residues: 922.9693 Evaluate side-chains 745 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 677 time to evaluate : 6.248 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: 68 outliers final: 7 residues processed: 68 average time/residue: 0.5054 time to fit residues: 74.2745 ------------------------------------------------------------------------------- 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: 0.0870 chunk 334 optimal weight: 20.0000 chunk 499 optimal weight: 0.9990 chunk 252 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 531 optimal weight: 9.9990 chunk 569 optimal weight: 20.0000 chunk 413 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 657 optimal weight: 0.9980 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A 438 HIS ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** 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 881 HIS ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN ** E 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1224 HIS ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 562 ASN ** G 640 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 562 ASN ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1224 HIS ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 454 GLN K 640 GLN ** K1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5305 moved from start: 0.6758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.154 71806 Z= 0.197 Angle : 0.662 11.779 97216 Z= 0.327 Chirality : 0.041 0.253 10731 Planarity : 0.004 0.150 12306 Dihedral : 6.483 149.744 9338 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.02 % Favored : 92.13 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.09), residues: 8708 helix: 0.44 (0.11), residues: 2352 sheet: -1.66 (0.11), residues: 1673 loop : -1.39 (0.09), residues: 4683 *********************** 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 816 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 730 time to evaluate : 6.387 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 outliers start: 86 outliers final: 42 residues processed: 795 average time/residue: 0.6360 time to fit residues: 904.2876 Evaluate side-chains 713 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 671 time to evaluate : 6.425 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: 42 outliers final: 7 residues processed: 42 average time/residue: 0.5362 time to fit residues: 51.6934 ------------------------------------------------------------------------------- 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: 0.0170 chunk 801 optimal weight: 7.9990 chunk 731 optimal weight: 0.9990 chunk 779 optimal weight: 0.9990 chunk 469 optimal weight: 20.0000 chunk 339 optimal weight: 8.9990 chunk 612 optimal weight: 0.6980 chunk 239 optimal weight: 7.9990 chunk 704 optimal weight: 8.9990 chunk 737 optimal weight: 30.0000 chunk 776 optimal weight: 0.9990 overall best weight: 0.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 562 ASN ** C 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1126 HIS ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 737 ASN ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 640 GLN ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1126 HIS I 438 HIS I1126 HIS ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 GLN K 454 GLN K 485 ASN ** K1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1055 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5274 moved from start: 0.6949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.113 71806 Z= 0.177 Angle : 0.660 11.870 97216 Z= 0.325 Chirality : 0.041 0.311 10731 Planarity : 0.004 0.153 12306 Dihedral : 6.344 143.629 9338 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.04 % Favored : 92.13 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.09), residues: 8708 helix: 0.59 (0.11), residues: 2296 sheet: -1.52 (0.11), residues: 1708 loop : -1.42 (0.09), residues: 4704 *********************** 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 789 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 733 time to evaluate : 6.559 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: 56 outliers final: 32 residues processed: 765 average time/residue: 0.6167 time to fit residues: 838.7598 Evaluate side-chains 703 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 671 time to evaluate : 6.259 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: 32 outliers final: 7 residues processed: 32 average time/residue: 0.5208 time to fit residues: 40.4659 ------------------------------------------------------------------------------- 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: 0.4980 chunk 824 optimal weight: 5.9990 chunk 503 optimal weight: 0.4980 chunk 391 optimal weight: 0.8980 chunk 573 optimal weight: 6.9990 chunk 864 optimal weight: 10.0000 chunk 795 optimal weight: 10.0000 chunk 688 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 531 optimal weight: 0.9980 chunk 422 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** 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 ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5272 moved from start: 0.7095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.137 71806 Z= 0.190 Angle : 0.668 13.483 97216 Z= 0.329 Chirality : 0.041 0.269 10731 Planarity : 0.005 0.160 12306 Dihedral : 6.265 142.443 9338 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.78 % Allowed : 7.14 % Favored : 92.08 % Rotamer Outliers : 0.33 % 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: -1.37 (0.09), residues: 8708 helix: 0.49 (0.11), residues: 2303 sheet: -1.41 (0.11), residues: 1743 loop : -1.42 (0.09), residues: 4662 ********************** 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 750 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 724 time to evaluate : 6.329 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: 26 outliers final: 16 residues processed: 738 average time/residue: 0.6219 time to fit residues: 816.0795 Evaluate side-chains 693 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 677 time to evaluate : 6.287 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: 16 outliers final: 7 residues processed: 16 average time/residue: 0.5391 time to fit residues: 25.1333 ------------------------------------------------------------------------------- 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: 4.9990 chunk 733 optimal weight: 8.9990 chunk 210 optimal weight: 0.0970 chunk 634 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 191 optimal weight: 30.0000 chunk 689 optimal weight: 4.9990 chunk 288 optimal weight: 0.3980 chunk 708 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 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 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 844 GLN ** G1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 737 ASN ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 HIS ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 545 GLN ** K1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 747 ASN M 844 GLN M1055 ASN ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.207025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.176394 restraints weight = 145084.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.179438 restraints weight = 258757.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.173933 restraints weight = 148883.238| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.7214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.136 71806 Z= 0.191 Angle : 0.664 14.001 97216 Z= 0.327 Chirality : 0.041 0.249 10731 Planarity : 0.005 0.156 12306 Dihedral : 6.186 142.790 9338 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.18 % Favored : 92.02 % Rotamer Outliers : 0.44 % 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: -1.31 (0.09), residues: 8708 helix: 0.54 (0.11), residues: 2289 sheet: -1.34 (0.12), residues: 1743 loop : -1.39 (0.09), residues: 4676 =============================================================================== Job complete usr+sys time: 17896.63 seconds wall clock time: 315 minutes 45.52 seconds (18945.52 seconds total)