Starting phenix.real_space_refine on Fri Dec 8 11:14:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6i_4468/12_2023/6q6i_4468_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6i_4468/12_2023/6q6i_4468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6i_4468/12_2023/6q6i_4468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6i_4468/12_2023/6q6i_4468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6i_4468/12_2023/6q6i_4468_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6i_4468/12_2023/6q6i_4468_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 230 5.16 5 C 36400 2.51 5 N 9990 2.21 5 O 10570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 24": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B GLU 339": "OE1" <-> "OE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B GLU 518": "OE1" <-> "OE2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B GLU 714": "OE1" <-> "OE2" Residue "B ARG 721": "NH1" <-> "NH2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C GLU 447": "OE1" <-> "OE2" Residue "C GLU 518": "OE1" <-> "OE2" Residue "C ARG 553": "NH1" <-> "NH2" Residue "C GLU 557": "OE1" <-> "OE2" Residue "C GLU 714": "OE1" <-> "OE2" Residue "C ARG 721": "NH1" <-> "NH2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "D GLU 447": "OE1" <-> "OE2" Residue "D GLU 518": "OE1" <-> "OE2" Residue "D ARG 553": "NH1" <-> "NH2" Residue "D GLU 557": "OE1" <-> "OE2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D ARG 721": "NH1" <-> "NH2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E GLU 192": "OE1" <-> "OE2" Residue "E ARG 196": "NH1" <-> "NH2" Residue "E ARG 253": "NH1" <-> "NH2" Residue "E GLU 339": "OE1" <-> "OE2" Residue "E GLU 447": "OE1" <-> "OE2" Residue "E GLU 518": "OE1" <-> "OE2" Residue "E ARG 553": "NH1" <-> "NH2" Residue "E GLU 557": "OE1" <-> "OE2" Residue "E GLU 714": "OE1" <-> "OE2" Residue "E ARG 721": "NH1" <-> "NH2" Residue "F GLU 24": "OE1" <-> "OE2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F ARG 196": "NH1" <-> "NH2" Residue "F ARG 253": "NH1" <-> "NH2" Residue "F GLU 339": "OE1" <-> "OE2" Residue "F GLU 447": "OE1" <-> "OE2" Residue "F GLU 518": "OE1" <-> "OE2" Residue "F ARG 553": "NH1" <-> "NH2" Residue "F GLU 557": "OE1" <-> "OE2" Residue "F GLU 714": "OE1" <-> "OE2" Residue "F ARG 721": "NH1" <-> "NH2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 192": "OE1" <-> "OE2" Residue "G ARG 196": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 339": "OE1" <-> "OE2" Residue "G GLU 447": "OE1" <-> "OE2" Residue "G GLU 518": "OE1" <-> "OE2" Residue "G ARG 553": "NH1" <-> "NH2" Residue "G GLU 557": "OE1" <-> "OE2" Residue "G GLU 714": "OE1" <-> "OE2" Residue "G ARG 721": "NH1" <-> "NH2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H ARG 196": "NH1" <-> "NH2" Residue "H ARG 253": "NH1" <-> "NH2" Residue "H GLU 339": "OE1" <-> "OE2" Residue "H GLU 447": "OE1" <-> "OE2" Residue "H GLU 518": "OE1" <-> "OE2" Residue "H ARG 553": "NH1" <-> "NH2" Residue "H GLU 557": "OE1" <-> "OE2" Residue "H GLU 714": "OE1" <-> "OE2" Residue "H ARG 721": "NH1" <-> "NH2" Residue "I GLU 24": "OE1" <-> "OE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "I GLU 192": "OE1" <-> "OE2" Residue "I ARG 196": "NH1" <-> "NH2" Residue "I ARG 253": "NH1" <-> "NH2" Residue "I GLU 339": "OE1" <-> "OE2" Residue "I GLU 447": "OE1" <-> "OE2" Residue "I GLU 518": "OE1" <-> "OE2" Residue "I ARG 553": "NH1" <-> "NH2" Residue "I GLU 557": "OE1" <-> "OE2" Residue "I GLU 714": "OE1" <-> "OE2" Residue "I ARG 721": "NH1" <-> "NH2" Residue "J GLU 24": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 110": "OE1" <-> "OE2" Residue "J GLU 192": "OE1" <-> "OE2" Residue "J ARG 196": "NH1" <-> "NH2" Residue "J ARG 253": "NH1" <-> "NH2" Residue "J GLU 339": "OE1" <-> "OE2" Residue "J GLU 447": "OE1" <-> "OE2" Residue "J GLU 518": "OE1" <-> "OE2" Residue "J ARG 553": "NH1" <-> "NH2" Residue "J GLU 557": "OE1" <-> "OE2" Residue "J GLU 714": "OE1" <-> "OE2" Residue "J ARG 721": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 57200 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS A 750 " pdbres="PLP A 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS B 750 " pdbres="PLP B 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS C 750 " pdbres="PLP C 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS D 750 " pdbres="PLP D 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS E 750 " pdbres="PLP E 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "F" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS F 750 " pdbres="PLP F 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS G 750 " pdbres="PLP G 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "H" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS H 750 " pdbres="PLP H 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "I" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS I 750 " pdbres="PLP I 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "J" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS J 750 " pdbres="PLP J 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Time building chain proxies: 21.92, per 1000 atoms: 0.38 Number of scatterers: 57200 At special positions: 0 Unit cell: (189.198, 193.275, 103.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 230 16.00 P 10 15.00 O 10570 8.00 N 9990 7.00 C 36400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.51 Conformation dependent library (CDL) restraints added in 7.8 seconds 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 280 helices and 50 sheets defined 29.4% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.84 Creating SS restraints... Processing helix chain 'A' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 52 No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 76 through 86 Processing helix chain 'A' and resid 129 through 146 Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA A 217 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.629A pdb=" N THR A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 441 Processing helix chain 'A' and resid 448 through 462 removed outlier: 4.033A pdb=" N GLY A 451 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER A 453 " --> pdb=" O ALA A 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 455 " --> pdb=" O ARG A 452 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN A 456 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 459 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 461 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 555 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 591 Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 603 through 606 No H-bonds generated for 'chain 'A' and resid 603 through 606' Processing helix chain 'A' and resid 623 through 633 removed outlier: 3.633A pdb=" N ALA A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 648 removed outlier: 3.805A pdb=" N LYS A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 647 " --> pdb=" O MET A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 665 No H-bonds generated for 'chain 'A' and resid 662 through 665' Processing helix chain 'A' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU A 714 " --> pdb=" O ASP A 711 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 717 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 718 " --> pdb=" O PHE A 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 719 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 721 " --> pdb=" O THR A 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 722 " --> pdb=" O PHE A 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU B 33 " --> pdb=" O ILE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 52 No H-bonds generated for 'chain 'B' and resid 49 through 52' Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 129 through 146 Processing helix chain 'B' and resid 150 through 156 Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 181 through 190 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA B 217 " --> pdb=" O GLY B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 274 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.629A pdb=" N THR B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 441 Processing helix chain 'B' and resid 448 through 462 removed outlier: 4.033A pdb=" N GLY B 451 " --> pdb=" O GLY B 448 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER B 453 " --> pdb=" O ALA B 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 455 " --> pdb=" O ARG B 452 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN B 456 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 459 " --> pdb=" O GLN B 456 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 461 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA B 470 " --> pdb=" O ARG B 466 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 558 removed outlier: 3.696A pdb=" N SER B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 555 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 557 " --> pdb=" O ARG B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 591 Processing helix chain 'B' and resid 593 through 595 No H-bonds generated for 'chain 'B' and resid 593 through 595' Processing helix chain 'B' and resid 603 through 606 No H-bonds generated for 'chain 'B' and resid 603 through 606' Processing helix chain 'B' and resid 623 through 633 removed outlier: 3.633A pdb=" N ALA B 632 " --> pdb=" O ASP B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 648 removed outlier: 3.804A pdb=" N LYS B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 647 " --> pdb=" O MET B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 665 No H-bonds generated for 'chain 'B' and resid 662 through 665' Processing helix chain 'B' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU B 714 " --> pdb=" O ASP B 711 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B 717 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 718 " --> pdb=" O PHE B 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 719 " --> pdb=" O ALA B 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 721 " --> pdb=" O THR B 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 722 " --> pdb=" O PHE B 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU C 33 " --> pdb=" O ILE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 52 No H-bonds generated for 'chain 'C' and resid 49 through 52' Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 129 through 146 Processing helix chain 'C' and resid 150 through 156 Processing helix chain 'C' and resid 176 through 178 No H-bonds generated for 'chain 'C' and resid 176 through 178' Processing helix chain 'C' and resid 181 through 190 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA C 217 " --> pdb=" O GLY C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS C 244 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 274 Processing helix chain 'C' and resid 296 through 298 No H-bonds generated for 'chain 'C' and resid 296 through 298' Processing helix chain 'C' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.629A pdb=" N THR C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 420 through 426 removed outlier: 5.401A pdb=" N MET C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 441 Processing helix chain 'C' and resid 448 through 462 removed outlier: 4.033A pdb=" N GLY C 451 " --> pdb=" O GLY C 448 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER C 453 " --> pdb=" O ALA C 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE C 455 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN C 456 " --> pdb=" O SER C 453 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 459 " --> pdb=" O GLN C 456 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 461 " --> pdb=" O THR C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA C 470 " --> pdb=" O ARG C 466 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL C 472 " --> pdb=" O ALA C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER C 552 " --> pdb=" O ALA C 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU C 555 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU C 557 " --> pdb=" O ARG C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 591 Processing helix chain 'C' and resid 593 through 595 No H-bonds generated for 'chain 'C' and resid 593 through 595' Processing helix chain 'C' and resid 603 through 606 No H-bonds generated for 'chain 'C' and resid 603 through 606' Processing helix chain 'C' and resid 623 through 633 removed outlier: 3.633A pdb=" N ALA C 632 " --> pdb=" O ASP C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 648 removed outlier: 3.805A pdb=" N LYS C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR C 647 " --> pdb=" O MET C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 665 No H-bonds generated for 'chain 'C' and resid 662 through 665' Processing helix chain 'C' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU C 714 " --> pdb=" O ASP C 711 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 717 " --> pdb=" O GLU C 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 718 " --> pdb=" O PHE C 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C 719 " --> pdb=" O ALA C 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 721 " --> pdb=" O THR C 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 722 " --> pdb=" O PHE C 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU D 33 " --> pdb=" O ILE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 52 No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 76 through 86 Processing helix chain 'D' and resid 129 through 146 Processing helix chain 'D' and resid 150 through 156 Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 214 through 219 removed outlier: 3.629A pdb=" N ALA D 217 " --> pdb=" O GLY D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 227 Processing helix chain 'D' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 274 Processing helix chain 'D' and resid 296 through 298 No H-bonds generated for 'chain 'D' and resid 296 through 298' Processing helix chain 'D' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 345 removed outlier: 3.630A pdb=" N THR D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N HIS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 441 Processing helix chain 'D' and resid 448 through 462 removed outlier: 4.032A pdb=" N GLY D 451 " --> pdb=" O GLY D 448 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG D 452 " --> pdb=" O PRO D 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER D 453 " --> pdb=" O ALA D 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE D 455 " --> pdb=" O ARG D 452 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN D 456 " --> pdb=" O SER D 453 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE D 459 " --> pdb=" O GLN D 456 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 461 " --> pdb=" O THR D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA D 470 " --> pdb=" O ARG D 466 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER D 552 " --> pdb=" O ALA D 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU D 555 " --> pdb=" O VAL D 551 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 557 " --> pdb=" O ARG D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 591 Processing helix chain 'D' and resid 593 through 595 No H-bonds generated for 'chain 'D' and resid 593 through 595' Processing helix chain 'D' and resid 603 through 606 No H-bonds generated for 'chain 'D' and resid 603 through 606' Processing helix chain 'D' and resid 623 through 633 removed outlier: 3.634A pdb=" N ALA D 632 " --> pdb=" O ASP D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 648 removed outlier: 3.805A pdb=" N LYS D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR D 647 " --> pdb=" O MET D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 665 No H-bonds generated for 'chain 'D' and resid 662 through 665' Processing helix chain 'D' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU D 714 " --> pdb=" O ASP D 711 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG D 717 " --> pdb=" O GLU D 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 718 " --> pdb=" O PHE D 715 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 719 " --> pdb=" O ALA D 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 721 " --> pdb=" O THR D 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 722 " --> pdb=" O PHE D 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU E 33 " --> pdb=" O ILE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 52 No H-bonds generated for 'chain 'E' and resid 49 through 52' Processing helix chain 'E' and resid 76 through 86 Processing helix chain 'E' and resid 129 through 146 Processing helix chain 'E' and resid 150 through 156 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 181 through 190 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA E 217 " --> pdb=" O GLY E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 227 Processing helix chain 'E' and resid 239 through 248 removed outlier: 4.386A pdb=" N LYS E 244 " --> pdb=" O SER E 240 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 274 Processing helix chain 'E' and resid 296 through 298 No H-bonds generated for 'chain 'E' and resid 296 through 298' Processing helix chain 'E' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA E 309 " --> pdb=" O ALA E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 345 removed outlier: 3.630A pdb=" N THR E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 441 Processing helix chain 'E' and resid 448 through 462 removed outlier: 4.033A pdb=" N GLY E 451 " --> pdb=" O GLY E 448 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG E 452 " --> pdb=" O PRO E 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER E 453 " --> pdb=" O ALA E 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE E 455 " --> pdb=" O ARG E 452 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN E 456 " --> pdb=" O SER E 453 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE E 459 " --> pdb=" O GLN E 456 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU E 461 " --> pdb=" O THR E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 472 removed outlier: 3.731A pdb=" N ALA E 470 " --> pdb=" O ARG E 466 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL E 472 " --> pdb=" O ALA E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER E 552 " --> pdb=" O ALA E 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU E 555 " --> pdb=" O VAL E 551 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU E 557 " --> pdb=" O ARG E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 591 Processing helix chain 'E' and resid 593 through 595 No H-bonds generated for 'chain 'E' and resid 593 through 595' Processing helix chain 'E' and resid 603 through 606 No H-bonds generated for 'chain 'E' and resid 603 through 606' Processing helix chain 'E' and resid 623 through 633 removed outlier: 3.634A pdb=" N ALA E 632 " --> pdb=" O ASP E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 648 removed outlier: 3.805A pdb=" N LYS E 644 " --> pdb=" O ALA E 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR E 647 " --> pdb=" O MET E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 665 No H-bonds generated for 'chain 'E' and resid 662 through 665' Processing helix chain 'E' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU E 714 " --> pdb=" O ASP E 711 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG E 717 " --> pdb=" O GLU E 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 718 " --> pdb=" O PHE E 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE E 719 " --> pdb=" O ALA E 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG E 721 " --> pdb=" O THR E 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA E 722 " --> pdb=" O PHE E 719 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 52 No H-bonds generated for 'chain 'F' and resid 49 through 52' Processing helix chain 'F' and resid 76 through 86 Processing helix chain 'F' and resid 129 through 146 Processing helix chain 'F' and resid 150 through 156 Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 181 through 190 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA F 217 " --> pdb=" O GLY F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 227 Processing helix chain 'F' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS F 244 " --> pdb=" O SER F 240 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL F 246 " --> pdb=" O ALA F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 274 Processing helix chain 'F' and resid 296 through 298 No H-bonds generated for 'chain 'F' and resid 296 through 298' Processing helix chain 'F' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA F 309 " --> pdb=" O ALA F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 removed outlier: 3.629A pdb=" N THR F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 441 Processing helix chain 'F' and resid 448 through 462 removed outlier: 4.033A pdb=" N GLY F 451 " --> pdb=" O GLY F 448 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG F 452 " --> pdb=" O PRO F 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER F 453 " --> pdb=" O ALA F 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE F 455 " --> pdb=" O ARG F 452 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN F 456 " --> pdb=" O SER F 453 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE F 459 " --> pdb=" O GLN F 456 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 461 " --> pdb=" O THR F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA F 470 " --> pdb=" O ARG F 466 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL F 472 " --> pdb=" O ALA F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER F 552 " --> pdb=" O ALA F 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU F 555 " --> pdb=" O VAL F 551 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 557 " --> pdb=" O ARG F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 591 Processing helix chain 'F' and resid 593 through 595 No H-bonds generated for 'chain 'F' and resid 593 through 595' Processing helix chain 'F' and resid 603 through 606 No H-bonds generated for 'chain 'F' and resid 603 through 606' Processing helix chain 'F' and resid 623 through 633 removed outlier: 3.633A pdb=" N ALA F 632 " --> pdb=" O ASP F 628 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 648 removed outlier: 3.805A pdb=" N LYS F 644 " --> pdb=" O ALA F 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR F 647 " --> pdb=" O MET F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 665 No H-bonds generated for 'chain 'F' and resid 662 through 665' Processing helix chain 'F' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU F 714 " --> pdb=" O ASP F 711 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG F 717 " --> pdb=" O GLU F 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR F 718 " --> pdb=" O PHE F 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE F 719 " --> pdb=" O ALA F 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG F 721 " --> pdb=" O THR F 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA F 722 " --> pdb=" O PHE F 719 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU G 33 " --> pdb=" O ILE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 52 No H-bonds generated for 'chain 'G' and resid 49 through 52' Processing helix chain 'G' and resid 76 through 86 Processing helix chain 'G' and resid 129 through 146 Processing helix chain 'G' and resid 150 through 156 Processing helix chain 'G' and resid 176 through 178 No H-bonds generated for 'chain 'G' and resid 176 through 178' Processing helix chain 'G' and resid 181 through 190 Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA G 217 " --> pdb=" O GLY G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 227 Processing helix chain 'G' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS G 244 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL G 246 " --> pdb=" O ALA G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 274 Processing helix chain 'G' and resid 296 through 298 No H-bonds generated for 'chain 'G' and resid 296 through 298' Processing helix chain 'G' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA G 309 " --> pdb=" O ALA G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 345 removed outlier: 3.629A pdb=" N THR G 344 " --> pdb=" O LEU G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 364 No H-bonds generated for 'chain 'G' and resid 362 through 364' Processing helix chain 'G' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET G 425 " --> pdb=" O GLU G 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS G 426 " --> pdb=" O ALA G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 441 Processing helix chain 'G' and resid 448 through 462 removed outlier: 4.033A pdb=" N GLY G 451 " --> pdb=" O GLY G 448 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG G 452 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER G 453 " --> pdb=" O ALA G 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE G 455 " --> pdb=" O ARG G 452 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN G 456 " --> pdb=" O SER G 453 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE G 459 " --> pdb=" O GLN G 456 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU G 461 " --> pdb=" O THR G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA G 470 " --> pdb=" O ARG G 466 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL G 472 " --> pdb=" O ALA G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 548 through 558 removed outlier: 3.696A pdb=" N SER G 552 " --> pdb=" O ALA G 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU G 555 " --> pdb=" O VAL G 551 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU G 557 " --> pdb=" O ARG G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 591 Processing helix chain 'G' and resid 593 through 595 No H-bonds generated for 'chain 'G' and resid 593 through 595' Processing helix chain 'G' and resid 603 through 606 No H-bonds generated for 'chain 'G' and resid 603 through 606' Processing helix chain 'G' and resid 623 through 633 removed outlier: 3.633A pdb=" N ALA G 632 " --> pdb=" O ASP G 628 " (cutoff:3.500A) Processing helix chain 'G' and resid 639 through 648 removed outlier: 3.804A pdb=" N LYS G 644 " --> pdb=" O ALA G 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR G 647 " --> pdb=" O MET G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 662 through 665 No H-bonds generated for 'chain 'G' and resid 662 through 665' Processing helix chain 'G' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU G 714 " --> pdb=" O ASP G 711 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG G 717 " --> pdb=" O GLU G 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR G 718 " --> pdb=" O PHE G 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE G 719 " --> pdb=" O ALA G 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG G 721 " --> pdb=" O THR G 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA G 722 " --> pdb=" O PHE G 719 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU H 33 " --> pdb=" O ILE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 52 No H-bonds generated for 'chain 'H' and resid 49 through 52' Processing helix chain 'H' and resid 76 through 86 Processing helix chain 'H' and resid 129 through 146 Processing helix chain 'H' and resid 150 through 156 Processing helix chain 'H' and resid 176 through 178 No H-bonds generated for 'chain 'H' and resid 176 through 178' Processing helix chain 'H' and resid 181 through 190 Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA H 217 " --> pdb=" O GLY H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 227 Processing helix chain 'H' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS H 244 " --> pdb=" O SER H 240 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL H 246 " --> pdb=" O ALA H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 274 Processing helix chain 'H' and resid 296 through 298 No H-bonds generated for 'chain 'H' and resid 296 through 298' Processing helix chain 'H' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA H 309 " --> pdb=" O ALA H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 345 removed outlier: 3.630A pdb=" N THR H 344 " --> pdb=" O LEU H 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 364 No H-bonds generated for 'chain 'H' and resid 362 through 364' Processing helix chain 'H' and resid 420 through 426 removed outlier: 5.401A pdb=" N MET H 425 " --> pdb=" O GLU H 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS H 426 " --> pdb=" O ALA H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 441 Processing helix chain 'H' and resid 448 through 462 removed outlier: 4.032A pdb=" N GLY H 451 " --> pdb=" O GLY H 448 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG H 452 " --> pdb=" O PRO H 449 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER H 453 " --> pdb=" O ALA H 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE H 455 " --> pdb=" O ARG H 452 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN H 456 " --> pdb=" O SER H 453 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE H 459 " --> pdb=" O GLN H 456 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU H 461 " --> pdb=" O THR H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA H 470 " --> pdb=" O ARG H 466 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL H 472 " --> pdb=" O ALA H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER H 552 " --> pdb=" O ALA H 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU H 555 " --> pdb=" O VAL H 551 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU H 557 " --> pdb=" O ARG H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 583 through 591 Processing helix chain 'H' and resid 593 through 595 No H-bonds generated for 'chain 'H' and resid 593 through 595' Processing helix chain 'H' and resid 603 through 606 No H-bonds generated for 'chain 'H' and resid 603 through 606' Processing helix chain 'H' and resid 623 through 633 removed outlier: 3.633A pdb=" N ALA H 632 " --> pdb=" O ASP H 628 " (cutoff:3.500A) Processing helix chain 'H' and resid 639 through 648 removed outlier: 3.804A pdb=" N LYS H 644 " --> pdb=" O ALA H 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR H 647 " --> pdb=" O MET H 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 662 through 665 No H-bonds generated for 'chain 'H' and resid 662 through 665' Processing helix chain 'H' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU H 714 " --> pdb=" O ASP H 711 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG H 717 " --> pdb=" O GLU H 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR H 718 " --> pdb=" O PHE H 715 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE H 719 " --> pdb=" O ALA H 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG H 721 " --> pdb=" O THR H 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA H 722 " --> pdb=" O PHE H 719 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU I 33 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 52 No H-bonds generated for 'chain 'I' and resid 49 through 52' Processing helix chain 'I' and resid 76 through 86 Processing helix chain 'I' and resid 129 through 146 Processing helix chain 'I' and resid 150 through 156 Processing helix chain 'I' and resid 176 through 178 No H-bonds generated for 'chain 'I' and resid 176 through 178' Processing helix chain 'I' and resid 181 through 190 Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'I' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA I 217 " --> pdb=" O GLY I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 227 Processing helix chain 'I' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS I 244 " --> pdb=" O SER I 240 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL I 246 " --> pdb=" O ALA I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 274 Processing helix chain 'I' and resid 296 through 298 No H-bonds generated for 'chain 'I' and resid 296 through 298' Processing helix chain 'I' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA I 309 " --> pdb=" O ALA I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 345 removed outlier: 3.630A pdb=" N THR I 344 " --> pdb=" O LEU I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 364 No H-bonds generated for 'chain 'I' and resid 362 through 364' Processing helix chain 'I' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS I 426 " --> pdb=" O ALA I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 434 through 441 Processing helix chain 'I' and resid 448 through 462 removed outlier: 4.032A pdb=" N GLY I 451 " --> pdb=" O GLY I 448 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG I 452 " --> pdb=" O PRO I 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER I 453 " --> pdb=" O ALA I 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE I 455 " --> pdb=" O ARG I 452 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN I 456 " --> pdb=" O SER I 453 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE I 459 " --> pdb=" O GLN I 456 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU I 461 " --> pdb=" O THR I 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA I 470 " --> pdb=" O ARG I 466 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL I 472 " --> pdb=" O ALA I 468 " (cutoff:3.500A) Processing helix chain 'I' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER I 552 " --> pdb=" O ALA I 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU I 555 " --> pdb=" O VAL I 551 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU I 557 " --> pdb=" O ARG I 553 " (cutoff:3.500A) Processing helix chain 'I' and resid 583 through 591 Processing helix chain 'I' and resid 593 through 595 No H-bonds generated for 'chain 'I' and resid 593 through 595' Processing helix chain 'I' and resid 603 through 606 No H-bonds generated for 'chain 'I' and resid 603 through 606' Processing helix chain 'I' and resid 623 through 633 removed outlier: 3.634A pdb=" N ALA I 632 " --> pdb=" O ASP I 628 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 648 removed outlier: 3.805A pdb=" N LYS I 644 " --> pdb=" O ALA I 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR I 647 " --> pdb=" O MET I 643 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 665 No H-bonds generated for 'chain 'I' and resid 662 through 665' Processing helix chain 'I' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU I 714 " --> pdb=" O ASP I 711 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG I 717 " --> pdb=" O GLU I 714 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR I 718 " --> pdb=" O PHE I 715 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE I 719 " --> pdb=" O ALA I 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG I 721 " --> pdb=" O THR I 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA I 722 " --> pdb=" O PHE I 719 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU J 33 " --> pdb=" O ILE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 52 No H-bonds generated for 'chain 'J' and resid 49 through 52' Processing helix chain 'J' and resid 76 through 86 Processing helix chain 'J' and resid 129 through 146 Processing helix chain 'J' and resid 150 through 156 Processing helix chain 'J' and resid 176 through 178 No H-bonds generated for 'chain 'J' and resid 176 through 178' Processing helix chain 'J' and resid 181 through 190 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'J' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA J 217 " --> pdb=" O GLY J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 227 Processing helix chain 'J' and resid 239 through 248 removed outlier: 4.386A pdb=" N LYS J 244 " --> pdb=" O SER J 240 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL J 246 " --> pdb=" O ALA J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 274 Processing helix chain 'J' and resid 296 through 298 No H-bonds generated for 'chain 'J' and resid 296 through 298' Processing helix chain 'J' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA J 309 " --> pdb=" O ALA J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 345 removed outlier: 3.630A pdb=" N THR J 344 " --> pdb=" O LEU J 340 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 364 No H-bonds generated for 'chain 'J' and resid 362 through 364' Processing helix chain 'J' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET J 425 " --> pdb=" O GLU J 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS J 426 " --> pdb=" O ALA J 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 434 through 441 Processing helix chain 'J' and resid 448 through 462 removed outlier: 4.033A pdb=" N GLY J 451 " --> pdb=" O GLY J 448 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG J 452 " --> pdb=" O PRO J 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER J 453 " --> pdb=" O ALA J 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE J 455 " --> pdb=" O ARG J 452 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN J 456 " --> pdb=" O SER J 453 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE J 459 " --> pdb=" O GLN J 456 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU J 461 " --> pdb=" O THR J 458 " (cutoff:3.500A) Processing helix chain 'J' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA J 470 " --> pdb=" O ARG J 466 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL J 472 " --> pdb=" O ALA J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER J 552 " --> pdb=" O ALA J 548 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU J 555 " --> pdb=" O VAL J 551 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU J 557 " --> pdb=" O ARG J 553 " (cutoff:3.500A) Processing helix chain 'J' and resid 583 through 591 Processing helix chain 'J' and resid 593 through 595 No H-bonds generated for 'chain 'J' and resid 593 through 595' Processing helix chain 'J' and resid 603 through 606 No H-bonds generated for 'chain 'J' and resid 603 through 606' Processing helix chain 'J' and resid 623 through 633 removed outlier: 3.633A pdb=" N ALA J 632 " --> pdb=" O ASP J 628 " (cutoff:3.500A) Processing helix chain 'J' and resid 639 through 648 removed outlier: 3.804A pdb=" N LYS J 644 " --> pdb=" O ALA J 640 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR J 647 " --> pdb=" O MET J 643 " (cutoff:3.500A) Processing helix chain 'J' and resid 662 through 665 No H-bonds generated for 'chain 'J' and resid 662 through 665' Processing helix chain 'J' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU J 714 " --> pdb=" O ASP J 711 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG J 717 " --> pdb=" O GLU J 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR J 718 " --> pdb=" O PHE J 715 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE J 719 " --> pdb=" O ALA J 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG J 721 " --> pdb=" O THR J 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA J 722 " --> pdb=" O PHE J 719 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU A 10 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE A 62 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A 12 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL A 64 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL A 64 " --> pdb=" O PRO A 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE A 96 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 99 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU A 352 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR A 388 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE A 354 " --> pdb=" O THR A 388 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA A 324 " --> pdb=" O HIS A 353 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE A 277 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL A 259 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU A 279 " --> pdb=" O VAL A 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU A 530 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 669 through 673 removed outlier: 3.826A pdb=" N GLU A 670 " --> pdb=" O CYS A 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS A 748 " --> pdb=" O GLU A 670 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU B 10 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE B 62 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL B 12 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 64 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL B 64 " --> pdb=" O PRO B 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE B 96 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 99 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU B 352 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR B 388 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE B 354 " --> pdb=" O THR B 388 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA B 324 " --> pdb=" O HIS B 353 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE B 277 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL B 259 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU B 279 " --> pdb=" O VAL B 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU B 530 " --> pdb=" O PHE B 570 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 669 through 673 removed outlier: 3.827A pdb=" N GLU B 670 " --> pdb=" O CYS B 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS B 748 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU C 10 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE C 62 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL C 12 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL C 64 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL C 64 " --> pdb=" O PRO C 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE C 96 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY C 99 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 231 through 235 removed outlier: 6.291A pdb=" N LEU C 352 " --> pdb=" O PHE C 386 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR C 388 " --> pdb=" O LEU C 352 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE C 354 " --> pdb=" O THR C 388 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA C 324 " --> pdb=" O HIS C 353 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE C 277 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL C 259 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU C 279 " --> pdb=" O VAL C 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU C 530 " --> pdb=" O PHE C 570 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 669 through 673 removed outlier: 3.827A pdb=" N GLU C 670 " --> pdb=" O CYS C 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS C 748 " --> pdb=" O GLU C 670 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU D 10 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE D 62 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL D 12 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL D 64 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL D 64 " --> pdb=" O PRO D 94 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE D 96 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY D 99 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU D 352 " --> pdb=" O PHE D 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR D 388 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE D 354 " --> pdb=" O THR D 388 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA D 324 " --> pdb=" O HIS D 353 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE D 277 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL D 259 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU D 279 " --> pdb=" O VAL D 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU D 530 " --> pdb=" O PHE D 570 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 669 through 673 removed outlier: 3.826A pdb=" N GLU D 670 " --> pdb=" O CYS D 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS D 748 " --> pdb=" O GLU D 670 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU E 10 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE E 62 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL E 12 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL E 64 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL E 64 " --> pdb=" O PRO E 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE E 96 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY E 99 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU E 352 " --> pdb=" O PHE E 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR E 388 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE E 354 " --> pdb=" O THR E 388 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA E 324 " --> pdb=" O HIS E 353 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE E 277 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL E 259 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU E 279 " --> pdb=" O VAL E 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU E 530 " --> pdb=" O PHE E 570 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 669 through 673 removed outlier: 3.827A pdb=" N GLU E 670 " --> pdb=" O CYS E 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS E 748 " --> pdb=" O GLU E 670 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU F 10 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE F 62 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL F 12 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL F 64 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL F 64 " --> pdb=" O PRO F 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE F 96 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY F 99 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU F 352 " --> pdb=" O PHE F 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR F 388 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE F 354 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA F 324 " --> pdb=" O HIS F 353 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE F 277 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL F 259 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU F 279 " --> pdb=" O VAL F 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'F' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU F 530 " --> pdb=" O PHE F 570 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 669 through 673 removed outlier: 3.826A pdb=" N GLU F 670 " --> pdb=" O CYS F 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS F 748 " --> pdb=" O GLU F 670 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU G 10 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE G 62 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL G 12 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL G 64 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL G 64 " --> pdb=" O PRO G 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE G 96 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY G 99 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU G 352 " --> pdb=" O PHE G 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR G 388 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE G 354 " --> pdb=" O THR G 388 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA G 324 " --> pdb=" O HIS G 353 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE G 277 " --> pdb=" O VAL G 257 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL G 259 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU G 279 " --> pdb=" O VAL G 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'G' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU G 530 " --> pdb=" O PHE G 570 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 669 through 673 removed outlier: 3.827A pdb=" N GLU G 670 " --> pdb=" O CYS G 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS G 748 " --> pdb=" O GLU G 670 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU H 10 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE H 62 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL H 12 " --> pdb=" O ILE H 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL H 64 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL H 64 " --> pdb=" O PRO H 94 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE H 96 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY H 99 " --> pdb=" O LEU H 122 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU H 352 " --> pdb=" O PHE H 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR H 388 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE H 354 " --> pdb=" O THR H 388 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA H 324 " --> pdb=" O HIS H 353 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE H 277 " --> pdb=" O VAL H 257 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL H 259 " --> pdb=" O ILE H 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU H 279 " --> pdb=" O VAL H 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'H' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU H 530 " --> pdb=" O PHE H 570 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 669 through 673 removed outlier: 3.826A pdb=" N GLU H 670 " --> pdb=" O CYS H 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS H 748 " --> pdb=" O GLU H 670 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU I 10 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE I 62 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL I 12 " --> pdb=" O ILE I 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL I 64 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL I 64 " --> pdb=" O PRO I 94 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE I 96 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY I 99 " --> pdb=" O LEU I 122 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'I' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU I 352 " --> pdb=" O PHE I 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR I 388 " --> pdb=" O LEU I 352 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE I 354 " --> pdb=" O THR I 388 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA I 324 " --> pdb=" O HIS I 353 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'I' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE I 277 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL I 259 " --> pdb=" O ILE I 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU I 279 " --> pdb=" O VAL I 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'I' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU I 530 " --> pdb=" O PHE I 570 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'I' and resid 669 through 673 removed outlier: 3.826A pdb=" N GLU I 670 " --> pdb=" O CYS I 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS I 748 " --> pdb=" O GLU I 670 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'J' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU J 10 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE J 62 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL J 12 " --> pdb=" O ILE J 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL J 64 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL J 64 " --> pdb=" O PRO J 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE J 96 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY J 99 " --> pdb=" O LEU J 122 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'J' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU J 352 " --> pdb=" O PHE J 386 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR J 388 " --> pdb=" O LEU J 352 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE J 354 " --> pdb=" O THR J 388 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA J 324 " --> pdb=" O HIS J 353 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE J 277 " --> pdb=" O VAL J 257 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL J 259 " --> pdb=" O ILE J 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU J 279 " --> pdb=" O VAL J 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'J' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU J 530 " --> pdb=" O PHE J 570 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'J' and resid 669 through 673 removed outlier: 3.826A pdb=" N GLU J 670 " --> pdb=" O CYS J 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS J 748 " --> pdb=" O GLU J 670 " (cutoff:3.500A) 1030 hydrogen bonds defined for protein. 2640 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: 17.42 Time building geometry restraints manager: 18.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 17190 1.33 - 1.45: 10878 1.45 - 1.57: 30072 1.57 - 1.69: 0 1.69 - 1.81: 410 Bond restraints: 58550 Sorted by residual: bond pdb=" O4P PLP I 801 " pdb=" P PLP I 801 " ideal model delta sigma weight residual 1.610 1.780 -0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" O4P PLP D 801 " pdb=" P PLP D 801 " ideal model delta sigma weight residual 1.610 1.780 -0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" O4P PLP G 801 " pdb=" P PLP G 801 " ideal model delta sigma weight residual 1.610 1.780 -0.170 2.00e-02 2.50e+03 7.22e+01 bond pdb=" O4P PLP B 801 " pdb=" P PLP B 801 " ideal model delta sigma weight residual 1.610 1.780 -0.170 2.00e-02 2.50e+03 7.22e+01 bond pdb=" O4P PLP E 801 " pdb=" P PLP E 801 " ideal model delta sigma weight residual 1.610 1.780 -0.170 2.00e-02 2.50e+03 7.22e+01 ... (remaining 58545 not shown) Histogram of bond angle deviations from ideal: 97.35 - 104.72: 1214 104.72 - 112.10: 27581 112.10 - 119.48: 21424 119.48 - 126.86: 28431 126.86 - 134.23: 990 Bond angle restraints: 79640 Sorted by residual: angle pdb=" CA HIS G 392 " pdb=" C HIS G 392 " pdb=" N LYS G 393 " ideal model delta sigma weight residual 118.55 104.79 13.76 1.24e+00 6.50e-01 1.23e+02 angle pdb=" CA HIS D 392 " pdb=" C HIS D 392 " pdb=" N LYS D 393 " ideal model delta sigma weight residual 118.55 104.80 13.75 1.24e+00 6.50e-01 1.23e+02 angle pdb=" CA HIS I 392 " pdb=" C HIS I 392 " pdb=" N LYS I 393 " ideal model delta sigma weight residual 118.55 104.80 13.75 1.24e+00 6.50e-01 1.23e+02 angle pdb=" CA HIS E 392 " pdb=" C HIS E 392 " pdb=" N LYS E 393 " ideal model delta sigma weight residual 118.55 104.80 13.75 1.24e+00 6.50e-01 1.23e+02 angle pdb=" CA HIS H 392 " pdb=" C HIS H 392 " pdb=" N LYS H 393 " ideal model delta sigma weight residual 118.55 104.81 13.74 1.24e+00 6.50e-01 1.23e+02 ... (remaining 79635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.69: 31778 23.69 - 47.39: 2522 47.39 - 71.08: 220 71.08 - 94.78: 80 94.78 - 118.47: 10 Dihedral angle restraints: 34610 sinusoidal: 13150 harmonic: 21460 Sorted by residual: dihedral pdb=" CA VAL E 203 " pdb=" C VAL E 203 " pdb=" N PRO E 204 " pdb=" CA PRO E 204 " ideal model delta harmonic sigma weight residual -180.00 -133.23 -46.77 0 5.00e+00 4.00e-02 8.75e+01 dihedral pdb=" CA VAL J 203 " pdb=" C VAL J 203 " pdb=" N PRO J 204 " pdb=" CA PRO J 204 " ideal model delta harmonic sigma weight residual -180.00 -133.23 -46.77 0 5.00e+00 4.00e-02 8.75e+01 dihedral pdb=" CA VAL A 203 " pdb=" C VAL A 203 " pdb=" N PRO A 204 " pdb=" CA PRO A 204 " ideal model delta harmonic sigma weight residual 180.00 -133.24 -46.76 0 5.00e+00 4.00e-02 8.75e+01 ... (remaining 34607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 6649 0.066 - 0.131: 1963 0.131 - 0.197: 218 0.197 - 0.263: 40 0.263 - 0.328: 30 Chirality restraints: 8900 Sorted by residual: chirality pdb=" CA THR C 168 " pdb=" N THR C 168 " pdb=" C THR C 168 " pdb=" CB THR C 168 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA THR E 168 " pdb=" N THR E 168 " pdb=" C THR E 168 " pdb=" CB THR E 168 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA THR G 168 " pdb=" N THR G 168 " pdb=" C THR G 168 " pdb=" CB THR G 168 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 8897 not shown) Planarity restraints: 10360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS E 392 " -0.034 2.00e-02 2.50e+03 7.52e-02 5.65e+01 pdb=" C HIS E 392 " 0.130 2.00e-02 2.50e+03 pdb=" O HIS E 392 " -0.055 2.00e-02 2.50e+03 pdb=" N LYS E 393 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 392 " 0.034 2.00e-02 2.50e+03 7.51e-02 5.65e+01 pdb=" C HIS C 392 " -0.129 2.00e-02 2.50e+03 pdb=" O HIS C 392 " 0.055 2.00e-02 2.50e+03 pdb=" N LYS C 393 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 392 " 0.034 2.00e-02 2.50e+03 7.51e-02 5.64e+01 pdb=" C HIS D 392 " -0.129 2.00e-02 2.50e+03 pdb=" O HIS D 392 " 0.055 2.00e-02 2.50e+03 pdb=" N LYS D 393 " 0.041 2.00e-02 2.50e+03 ... (remaining 10357 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 13125 2.78 - 3.31: 52702 3.31 - 3.84: 97802 3.84 - 4.37: 114034 4.37 - 4.90: 189597 Nonbonded interactions: 467260 Sorted by model distance: nonbonded pdb=" O SER E 197 " pdb=" OG SER E 197 " model vdw 2.244 2.440 nonbonded pdb=" O SER C 197 " pdb=" OG SER C 197 " model vdw 2.245 2.440 nonbonded pdb=" O SER H 197 " pdb=" OG SER H 197 " model vdw 2.245 2.440 nonbonded pdb=" O SER I 197 " pdb=" OG SER I 197 " model vdw 2.245 2.440 nonbonded pdb=" O SER F 197 " pdb=" OG SER F 197 " model vdw 2.245 2.440 ... (remaining 467255 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 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: 12.120 Check model and map are aligned: 0.640 Set scattering table: 0.380 Process input model: 111.050 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 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 : 0.009 0.170 58550 Z= 0.585 Angle : 1.224 17.933 79640 Z= 0.649 Chirality : 0.063 0.328 8900 Planarity : 0.008 0.075 10360 Dihedral : 17.031 118.474 20850 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 16.71 % Favored : 83.03 % Rotamer: Outliers : 1.89 % Allowed : 15.32 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.56 % 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: -5.81 (0.07), residues: 7470 helix: -4.07 (0.06), residues: 2720 sheet: -4.11 (0.11), residues: 960 loop : -3.61 (0.08), residues: 3790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP B 486 HIS 0.008 0.002 HIS H 187 PHE 0.027 0.003 PHE J 570 TYR 0.062 0.004 TYR C 359 ARG 0.014 0.001 ARG E 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1482 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1372 time to evaluate : 4.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 48 residues processed: 1452 average time/residue: 0.5841 time to fit residues: 1395.1433 Evaluate side-chains 1068 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1020 time to evaluate : 4.546 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 10 residues processed: 48 average time/residue: 0.4881 time to fit residues: 47.8387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 633 optimal weight: 0.8980 chunk 568 optimal weight: 0.8980 chunk 315 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 383 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 587 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 357 optimal weight: 0.5980 chunk 437 optimal weight: 2.9990 chunk 681 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 171 HIS A 187 HIS A 243 ASN A 343 GLN A 365 HIS ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN A 420 ASN A 456 GLN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 171 HIS B 187 HIS B 243 ASN B 343 GLN B 365 HIS B 400 GLN B 456 GLN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 171 HIS C 187 HIS C 243 ASN C 343 GLN C 365 HIS ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN D 171 HIS D 187 HIS D 243 ASN D 343 GLN D 365 HIS ** D 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 GLN D 420 ASN D 456 GLN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN E 92 GLN E 171 HIS E 243 ASN E 343 GLN E 365 HIS ** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 400 GLN E 420 ASN E 456 GLN ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 GLN F 171 HIS F 187 HIS F 243 ASN F 343 GLN F 365 HIS ** F 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 GLN F 420 ASN F 456 GLN ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN G 171 HIS G 187 HIS G 243 ASN G 343 GLN G 365 HIS G 400 GLN G 456 GLN ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN H 171 HIS H 187 HIS H 243 ASN H 343 GLN H 365 HIS ** H 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 400 GLN ** H 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 456 GLN ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 GLN I 171 HIS I 187 HIS I 243 ASN I 343 GLN I 365 HIS ** I 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 400 GLN I 420 ASN I 456 GLN ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN J 171 HIS J 187 HIS J 243 ASN J 343 GLN J 365 HIS ** J 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 400 GLN J 420 ASN J 456 GLN ** J 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 86 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 58550 Z= 0.194 Angle : 0.728 14.801 79640 Z= 0.366 Chirality : 0.046 0.219 8900 Planarity : 0.006 0.075 10360 Dihedral : 7.725 68.465 8160 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 4.11 % Allowed : 19.83 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -4.88 (0.08), residues: 7470 helix: -3.26 (0.07), residues: 2700 sheet: -3.44 (0.13), residues: 860 loop : -3.20 (0.09), residues: 3910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 486 HIS 0.004 0.001 HIS C 187 PHE 0.014 0.001 PHE E 593 TYR 0.030 0.002 TYR J 359 ARG 0.007 0.000 ARG H 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1412 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1173 time to evaluate : 4.660 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 outliers start: 239 outliers final: 142 residues processed: 1292 average time/residue: 0.5825 time to fit residues: 1242.9114 Evaluate side-chains 1138 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 996 time to evaluate : 4.527 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 10 residues processed: 142 average time/residue: 0.4637 time to fit residues: 125.1550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 378 optimal weight: 9.9990 chunk 211 optimal weight: 50.0000 chunk 566 optimal weight: 10.0000 chunk 463 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 682 optimal weight: 9.9990 chunk 737 optimal weight: 6.9990 chunk 607 optimal weight: 6.9990 chunk 676 optimal weight: 7.9990 chunk 232 optimal weight: 7.9990 chunk 547 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN B 226 ASN B 262 ASN ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN C 135 GLN ** C 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 ASN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN D 262 ASN ** D 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 ASN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 HIS E 262 ASN ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 ASN ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 GLN ** F 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 471 ASN ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 GLN G 226 ASN G 262 ASN ** G 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 471 ASN ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN H 135 GLN ** H 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 471 ASN ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN I 262 ASN ** I 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 471 ASN ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 GLN J 262 ASN ** J 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 471 ASN ** J 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.089 58550 Z= 0.698 Angle : 1.021 13.919 79640 Z= 0.522 Chirality : 0.056 0.241 8900 Planarity : 0.008 0.085 10360 Dihedral : 8.605 55.923 8160 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 25.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 19.46 % Favored : 80.40 % Rotamer: Outliers : 6.23 % Allowed : 23.29 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.24 % 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: -4.92 (0.08), residues: 7470 helix: -3.06 (0.08), residues: 2810 sheet: -3.98 (0.13), residues: 860 loop : -3.27 (0.09), residues: 3800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP E 247 HIS 0.007 0.002 HIS A 167 PHE 0.031 0.004 PHE F 723 TYR 0.051 0.005 TYR I 359 ARG 0.010 0.001 ARG F 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1413 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 1051 time to evaluate : 4.583 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 outliers start: 362 outliers final: 220 residues processed: 1309 average time/residue: 0.5684 time to fit residues: 1272.1766 Evaluate side-chains 1198 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 978 time to evaluate : 4.570 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 220 outliers final: 10 residues processed: 220 average time/residue: 0.4583 time to fit residues: 192.2859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 674 optimal weight: 9.9990 chunk 512 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 325 optimal weight: 10.0000 chunk 458 optimal weight: 2.9990 chunk 684 optimal weight: 0.9990 chunk 724 optimal weight: 8.9990 chunk 357 optimal weight: 0.8980 chunk 648 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN B 471 ASN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 ASN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 ASN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 ASN ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN ** F 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 471 ASN ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN G 471 ASN ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 471 ASN ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 471 ASN ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 471 ASN ** J 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 58550 Z= 0.226 Angle : 0.758 12.210 79640 Z= 0.378 Chirality : 0.047 0.200 8900 Planarity : 0.006 0.077 10360 Dihedral : 7.606 52.131 8160 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.90 % Favored : 86.10 % Rotamer: Outliers : 3.05 % Allowed : 26.32 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -4.43 (0.09), residues: 7470 helix: -2.53 (0.09), residues: 2730 sheet: -3.64 (0.13), residues: 850 loop : -3.11 (0.09), residues: 3890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 166 HIS 0.004 0.001 HIS J 392 PHE 0.019 0.002 PHE E 554 TYR 0.047 0.002 TYR F 359 ARG 0.009 0.000 ARG H 371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1250 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1073 time to evaluate : 4.742 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 outliers start: 177 outliers final: 102 residues processed: 1168 average time/residue: 0.5782 time to fit residues: 1143.9567 Evaluate side-chains 1065 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 963 time to evaluate : 4.603 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 10 residues processed: 102 average time/residue: 0.4681 time to fit residues: 92.8636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 603 optimal weight: 8.9990 chunk 411 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 539 optimal weight: 1.9990 chunk 299 optimal weight: 20.0000 chunk 618 optimal weight: 1.9990 chunk 501 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 370 optimal weight: 9.9990 chunk 650 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN C 262 ASN ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 GLN ** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN H 262 ASN ** H 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN ** J 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 58550 Z= 0.289 Angle : 0.755 12.603 79640 Z= 0.377 Chirality : 0.048 0.221 8900 Planarity : 0.006 0.077 10360 Dihedral : 7.394 57.564 8160 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.17 % Favored : 83.83 % Rotamer: Outliers : 3.46 % Allowed : 28.30 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -4.23 (0.09), residues: 7470 helix: -2.32 (0.09), residues: 2730 sheet: -3.54 (0.14), residues: 840 loop : -3.04 (0.09), residues: 3900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 247 HIS 0.004 0.001 HIS A 13 PHE 0.017 0.002 PHE A 367 TYR 0.051 0.002 TYR D 359 ARG 0.011 0.000 ARG G 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1202 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1001 time to evaluate : 4.626 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 outliers start: 201 outliers final: 114 residues processed: 1133 average time/residue: 0.5602 time to fit residues: 1078.0835 Evaluate side-chains 1057 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 943 time to evaluate : 4.608 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 10 residues processed: 114 average time/residue: 0.4592 time to fit residues: 102.0249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6621 > 50: distance: 45 - 49: 27.953 distance: 49 - 50: 15.203 distance: 50 - 51: 38.544 distance: 51 - 52: 67.417 distance: 51 - 57: 40.838 distance: 53 - 55: 57.379 distance: 54 - 56: 57.181 distance: 57 - 58: 39.015 distance: 58 - 59: 40.833 distance: 58 - 61: 57.299 distance: 59 - 60: 53.020 distance: 63 - 64: 29.601 distance: 63 - 66: 41.146 distance: 64 - 67: 21.261 distance: 67 - 68: 24.835 distance: 68 - 69: 52.949 distance: 68 - 71: 10.569 distance: 69 - 70: 36.444 distance: 69 - 74: 34.928 distance: 71 - 72: 43.063 distance: 71 - 73: 60.111 distance: 74 - 75: 32.365 distance: 75 - 76: 4.359 distance: 75 - 78: 53.152 distance: 76 - 77: 58.958 distance: 76 - 82: 7.305 distance: 78 - 79: 24.028 distance: 79 - 80: 47.200 distance: 80 - 81: 39.822 distance: 82 - 83: 11.531 distance: 83 - 84: 43.434 distance: 83 - 86: 37.621 distance: 84 - 85: 56.543 distance: 84 - 90: 39.016 distance: 86 - 87: 26.443 distance: 87 - 88: 64.191 distance: 87 - 89: 48.964 distance: 90 - 91: 20.449 distance: 91 - 92: 44.364 distance: 91 - 94: 22.545 distance: 92 - 93: 41.800 distance: 92 - 97: 11.453 distance: 94 - 95: 52.881 distance: 94 - 96: 55.437 distance: 97 - 98: 41.818 distance: 97 - 103: 27.017 distance: 98 - 99: 24.606 distance: 98 - 101: 27.963 distance: 99 - 100: 44.089 distance: 99 - 104: 15.325 distance: 101 - 102: 23.943 distance: 102 - 103: 51.497 distance: 104 - 105: 45.103 distance: 105 - 106: 44.529 distance: 105 - 108: 58.269 distance: 106 - 107: 45.338 distance: 106 - 116: 6.296 distance: 108 - 109: 19.090 distance: 109 - 110: 32.676 distance: 109 - 111: 25.650 distance: 110 - 112: 42.998 distance: 111 - 113: 42.162 distance: 112 - 114: 36.357 distance: 113 - 114: 37.644 distance: 114 - 115: 43.862 distance: 116 - 117: 39.457 distance: 116 - 122: 35.408 distance: 117 - 118: 19.546 distance: 117 - 120: 58.522 distance: 118 - 119: 37.461 distance: 118 - 123: 34.738 distance: 120 - 121: 32.165 distance: 121 - 122: 51.817