Starting phenix.real_space_refine on Sun Mar 24 06:04:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0z_4702/03_2024/6r0z_4702_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0z_4702/03_2024/6r0z_4702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0z_4702/03_2024/6r0z_4702.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0z_4702/03_2024/6r0z_4702.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0z_4702/03_2024/6r0z_4702_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0z_4702/03_2024/6r0z_4702_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.018 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 103 5.16 5 C 25043 2.51 5 N 7295 2.21 5 O 7738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 532": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 460": "NH1" <-> "NH2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "C ARG 481": "NH1" <-> "NH2" Residue "C ARG 488": "NH1" <-> "NH2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C ARG 547": "NH1" <-> "NH2" Residue "C ARG 550": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "D ARG 341": "NH1" <-> "NH2" Residue "D ARG 410": "NH1" <-> "NH2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E ARG 274": "NH1" <-> "NH2" Residue "E ARG 280": "NH1" <-> "NH2" Residue "E ARG 281": "NH1" <-> "NH2" Residue "E ARG 360": "NH1" <-> "NH2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "E ARG 409": "NH1" <-> "NH2" Residue "E ARG 420": "NH1" <-> "NH2" Residue "F ARG 41": "NH1" <-> "NH2" Residue "F ARG 81": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 174": "NH1" <-> "NH2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "F ARG 280": "NH1" <-> "NH2" Residue "F ARG 297": "NH1" <-> "NH2" Residue "F ARG 341": "NH1" <-> "NH2" Residue "F ARG 372": "NH1" <-> "NH2" Residue "F ARG 409": "NH1" <-> "NH2" Residue "F ARG 410": "NH1" <-> "NH2" Residue "F ARG 420": "NH1" <-> "NH2" Residue "G ARG 8": "NH1" <-> "NH2" Residue "G ARG 103": "NH1" <-> "NH2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G ARG 139": "NH1" <-> "NH2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "G ARG 160": "NH1" <-> "NH2" Residue "G ARG 173": "NH1" <-> "NH2" Residue "G ARG 188": "NH1" <-> "NH2" Residue "G ARG 196": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "H ARG 14": "NH1" <-> "NH2" Residue "H ARG 57": "NH1" <-> "NH2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "H ARG 64": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I ARG 78": "NH1" <-> "NH2" Residue "I ARG 87": "NH1" <-> "NH2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J ARG 105": "NH1" <-> "NH2" Residue "J ARG 136": "NH1" <-> "NH2" Residue "J ARG 149": "NH1" <-> "NH2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "K ARG 74": "NH1" <-> "NH2" Residue "K ARG 89": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 58": "NH1" <-> "NH2" Residue "L ARG 72": "NH1" <-> "NH2" Residue "L ARG 76": "NH1" <-> "NH2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L ARG 88": "NH1" <-> "NH2" Residue "L ARG 136": "NH1" <-> "NH2" Residue "L ARG 173": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40184 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "B" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "D" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3600 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 433} Chain: "E" Number of atoms: 3616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3616 Classifications: {'peptide': 462} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 435} Chain: "F" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3608 Classifications: {'peptide': 461} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 434} Chain: "G" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1647 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 9, 'TRANS': 200} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 809 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "J" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 7, 'TRANS': 178} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 789 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "L" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 7, 'TRANS': 178} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 1575 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 12, 'TRANS': 307} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 979 Unresolved non-hydrogen angles: 1248 Unresolved non-hydrogen dihedrals: 791 Unresolved non-hydrogen chiralities: 95 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 15, 'GLU:plan': 26, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 566 Chain: "N" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 3185 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 517} Link IDs: {'PTRANS': 36, 'TRANS': 611} Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 2027 Unresolved non-hydrogen angles: 2625 Unresolved non-hydrogen dihedrals: 1711 Unresolved non-hydrogen chiralities: 211 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 12, 'TYR:plan': 18, 'ASN:plan1': 7, 'TRP:plan': 12, 'HIS:plan': 21, 'PHE:plan': 33, 'GLU:plan': 56, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 1071 Chain: "O" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Q" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 356 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "R" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "S" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "U" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "V" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "W" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "X" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 347 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Y" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Z" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {' MG': 1, 'ADP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 20.81, per 1000 atoms: 0.52 Number of scatterers: 40184 At special positions: 0 Unit cell: (146.475, 147.56, 259.315, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 4 15.00 Mg 1 11.99 O 7738 8.00 N 7295 7.00 C 25043 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=0, symmetry=0 Time building additional restraints: 14.69 Conformation dependent library (CDL) restraints added in 7.9 seconds 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10538 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 176 helices and 37 sheets defined 52.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.69 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 211 through 214 No H-bonds generated for 'chain 'A' and resid 211 through 214' Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 260 through 268 removed outlier: 3.617A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 296 through 314 removed outlier: 4.259A pdb=" N GLU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A 305 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY A 306 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 removed outlier: 4.139A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 352 through 362 removed outlier: 4.039A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 399 No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 470 removed outlier: 4.677A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 532 Processing helix chain 'A' and resid 545 through 549 Processing helix chain 'A' and resid 559 through 572 Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 212 through 215 No H-bonds generated for 'chain 'B' and resid 212 through 215' Processing helix chain 'B' and resid 234 through 243 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 315 removed outlier: 5.841A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 436 through 442 Processing helix chain 'B' and resid 447 through 471 removed outlier: 4.055A pdb=" N ALA B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 493 Processing helix chain 'B' and resid 509 through 532 removed outlier: 4.422A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 540 removed outlier: 3.903A pdb=" N LEU B 540 " --> pdb=" O ILE B 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 536 through 540' Processing helix chain 'B' and resid 545 through 549 Processing helix chain 'B' and resid 559 through 576 removed outlier: 4.071A pdb=" N PHE B 563 " --> pdb=" O PRO B 560 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLU B 564 " --> pdb=" O ALA B 561 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 572 " --> pdb=" O GLU B 569 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 573 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA B 576 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 259 through 271 Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 298 through 315 removed outlier: 3.923A pdb=" N ILE C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 354 through 362 Processing helix chain 'C' and resid 394 through 400 Processing helix chain 'C' and resid 412 through 415 No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 447 through 471 removed outlier: 4.405A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 493 Processing helix chain 'C' and resid 509 through 530 Processing helix chain 'C' and resid 536 through 541 removed outlier: 3.706A pdb=" N LEU C 540 " --> pdb=" O ILE C 536 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLN C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 536 through 541' Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 559 through 572 Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 160 through 168 Processing helix chain 'D' and resid 199 through 210 removed outlier: 4.007A pdb=" N GLU D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 248 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 285 through 295 removed outlier: 4.324A pdb=" N TYR D 288 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR D 293 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'D' and resid 375 through 396 removed outlier: 4.023A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG D 393 " --> pdb=" O GLY D 389 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 421 removed outlier: 4.321A pdb=" N ARG D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.904A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 161 through 167 Processing helix chain 'E' and resid 198 through 211 removed outlier: 4.310A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 248 Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 271 Processing helix chain 'E' and resid 285 through 295 removed outlier: 4.437A pdb=" N TYR E 288 " --> pdb=" O GLY E 285 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR E 293 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 330 Processing helix chain 'E' and resid 342 through 345 No H-bonds generated for 'chain 'E' and resid 342 through 345' Processing helix chain 'E' and resid 360 through 365 removed outlier: 4.365A pdb=" N ASN E 363 " --> pdb=" O ARG E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 396 Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 433 through 445 removed outlier: 4.916A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 461 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'F' and resid 136 through 140 Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 199 through 211 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 231 through 247 Proline residue: F 235 - end of helix removed outlier: 4.389A pdb=" N VAL F 241 " --> pdb=" O MET F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 272 Processing helix chain 'F' and resid 285 through 295 removed outlier: 4.183A pdb=" N TYR F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 291 " --> pdb=" O TYR F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 346 Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.682A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU F 395 " --> pdb=" O ASP F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 406 through 421 removed outlier: 3.572A pdb=" N TYR F 411 " --> pdb=" O ASN F 407 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 412 " --> pdb=" O ASP F 408 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP F 416 " --> pdb=" O LEU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 445 removed outlier: 4.247A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 462 Processing helix chain 'G' and resid 8 through 70 removed outlier: 3.637A pdb=" N LEU G 12 " --> pdb=" O ARG G 8 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 80 Processing helix chain 'G' and resid 123 through 168 removed outlier: 4.165A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 210 removed outlier: 3.741A pdb=" N LYS G 195 " --> pdb=" O THR G 191 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU G 208 " --> pdb=" O ARG G 204 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 15 Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 56 through 62 Processing helix chain 'H' and resid 77 through 81 Processing helix chain 'H' and resid 86 through 98 Processing helix chain 'I' and resid 19 through 104 removed outlier: 4.016A pdb=" N MET I 104 " --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 115 removed outlier: 3.756A pdb=" N ALA I 112 " --> pdb=" O ASP I 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 96 removed outlier: 3.999A pdb=" N GLU J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Proline residue: J 95 - end of helix Processing helix chain 'J' and resid 98 through 113 Proline residue: J 101 - end of helix removed outlier: 4.074A pdb=" N VAL J 104 " --> pdb=" O PRO J 101 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ARG J 105 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS J 106 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU J 107 " --> pdb=" O VAL J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 159 No H-bonds generated for 'chain 'J' and resid 157 through 159' Processing helix chain 'J' and resid 167 through 186 removed outlier: 5.487A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 106 removed outlier: 3.629A pdb=" N ARG K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 removed outlier: 3.604A pdb=" N LEU K 113 " --> pdb=" O GLU K 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 94 removed outlier: 3.677A pdb=" N GLU L 46 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG L 47 " --> pdb=" O GLN L 43 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN L 52 " --> pdb=" O ALA L 48 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU L 80 " --> pdb=" O ARG L 76 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 114 Processing helix chain 'L' and resid 129 through 131 No H-bonds generated for 'chain 'L' and resid 129 through 131' Processing helix chain 'L' and resid 134 through 136 No H-bonds generated for 'chain 'L' and resid 134 through 136' Processing helix chain 'L' and resid 167 through 186 removed outlier: 5.628A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU L 178 " --> pdb=" O ALA L 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 17 removed outlier: 3.829A pdb=" N ARG M 11 " --> pdb=" O TYR M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 29 removed outlier: 3.556A pdb=" N LEU M 29 " --> pdb=" O PHE M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 42 Processing helix chain 'M' and resid 44 through 48 removed outlier: 3.906A pdb=" N GLY M 47 " --> pdb=" O VAL M 44 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU M 48 " --> pdb=" O TYR M 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 44 through 48' Processing helix chain 'M' and resid 54 through 73 removed outlier: 4.800A pdb=" N ASP M 71 " --> pdb=" O LYS M 67 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU M 72 " --> pdb=" O LEU M 68 " (cutoff:3.500A) Proline residue: M 73 - end of helix Processing helix chain 'M' and resid 78 through 86 removed outlier: 3.797A pdb=" N LEU M 86 " --> pdb=" O GLU M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 105 Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 133 through 139 Processing helix chain 'M' and resid 146 through 154 Processing helix chain 'M' and resid 162 through 181 Processing helix chain 'M' and resid 188 through 206 Processing helix chain 'M' and resid 214 through 217 No H-bonds generated for 'chain 'M' and resid 214 through 217' Processing helix chain 'M' and resid 227 through 234 Processing helix chain 'M' and resid 238 through 243 Processing helix chain 'M' and resid 258 through 277 removed outlier: 3.971A pdb=" N GLY M 276 " --> pdb=" O GLU M 272 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 309 Processing helix chain 'M' and resid 317 through 319 No H-bonds generated for 'chain 'M' and resid 317 through 319' Processing helix chain 'N' and resid 14 through 26 Processing helix chain 'N' and resid 47 through 70 Processing helix chain 'N' and resid 84 through 128 Proline residue: N 93 - end of helix removed outlier: 3.853A pdb=" N TYR N 118 " --> pdb=" O LEU N 114 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLU N 120 " --> pdb=" O GLN N 116 " (cutoff:3.500A) Proline residue: N 121 - end of helix Processing helix chain 'N' and resid 150 through 159 removed outlier: 4.869A pdb=" N ALA N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU N 157 " --> pdb=" O VAL N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 196 Processing helix chain 'N' and resid 213 through 268 Proline residue: N 228 - end of helix removed outlier: 5.768A pdb=" N SER N 247 " --> pdb=" O ARG N 243 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N THR N 248 " --> pdb=" O GLU N 244 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU N 267 " --> pdb=" O LEU N 263 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU N 268 " --> pdb=" O LYS N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 284 through 296 Proline residue: N 288 - end of helix Processing helix chain 'N' and resid 328 through 334 removed outlier: 3.501A pdb=" N GLU N 331 " --> pdb=" O LYS N 328 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU N 332 " --> pdb=" O PRO N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 348 through 362 Proline residue: N 352 - end of helix Proline residue: N 356 - end of helix Processing helix chain 'N' and resid 366 through 384 Processing helix chain 'N' and resid 400 through 424 removed outlier: 3.986A pdb=" N TRP N 416 " --> pdb=" O TRP N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 460 through 488 Processing helix chain 'N' and resid 492 through 515 Processing helix chain 'N' and resid 525 through 542 Processing helix chain 'N' and resid 548 through 587 removed outlier: 4.678A pdb=" N HIS N 561 " --> pdb=" O HIS N 557 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE N 562 " --> pdb=" O ILE N 558 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ARG N 563 " --> pdb=" O LEU N 559 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE N 564 " --> pdb=" O SER N 560 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR N 565 " --> pdb=" O HIS N 561 " (cutoff:3.500A) Processing helix chain 'N' and resid 594 through 631 removed outlier: 5.239A pdb=" N LEU N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY N 615 " --> pdb=" O LEU N 611 " (cutoff:3.500A) Proline residue: N 620 - end of helix removed outlier: 4.059A pdb=" N PHE N 629 " --> pdb=" O TRP N 625 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR N 630 " --> pdb=" O VAL N 626 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 47 removed outlier: 3.533A pdb=" N LEU O 14 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 79 Proline residue: O 62 - end of helix removed outlier: 5.687A pdb=" N LEU O 65 " --> pdb=" O LEU O 61 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL O 66 " --> pdb=" O PRO O 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 47 removed outlier: 4.249A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 78 removed outlier: 3.766A pdb=" N PHE P 52 " --> pdb=" O ARG P 49 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLY P 53 " --> pdb=" O SER P 50 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR P 54 " --> pdb=" O ASN P 51 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU P 61 " --> pdb=" O PHE P 58 " (cutoff:3.500A) Proline residue: P 62 - end of helix removed outlier: 3.702A pdb=" N LEU P 65 " --> pdb=" O PRO P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 47 removed outlier: 4.053A pdb=" N ARG Q 36 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 78 Proline residue: Q 62 - end of helix removed outlier: 5.533A pdb=" N LEU Q 65 " --> pdb=" O LEU Q 61 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL Q 66 " --> pdb=" O PRO Q 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 47 removed outlier: 4.125A pdb=" N ARG R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 79 removed outlier: 3.994A pdb=" N PHE R 52 " --> pdb=" O ARG R 49 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLY R 53 " --> pdb=" O SER R 50 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU R 56 " --> pdb=" O GLY R 53 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU R 61 " --> pdb=" O PHE R 58 " (cutoff:3.500A) Proline residue: R 62 - end of helix removed outlier: 3.697A pdb=" N LEU R 65 " --> pdb=" O PRO R 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 47 removed outlier: 4.195A pdb=" N ARG S 36 " --> pdb=" O VAL S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 79 removed outlier: 3.581A pdb=" N PHE S 52 " --> pdb=" O ARG S 49 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY S 53 " --> pdb=" O SER S 50 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR S 54 " --> pdb=" O ASN S 51 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU S 61 " --> pdb=" O PHE S 58 " (cutoff:3.500A) Proline residue: S 62 - end of helix removed outlier: 3.852A pdb=" N LEU S 65 " --> pdb=" O PRO S 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 47 removed outlier: 4.543A pdb=" N ARG T 36 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 79 Proline residue: T 62 - end of helix removed outlier: 5.332A pdb=" N LEU T 65 " --> pdb=" O LEU T 61 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL T 66 " --> pdb=" O PRO T 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 47 removed outlier: 4.125A pdb=" N ARG U 36 " --> pdb=" O VAL U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 79 Proline residue: U 62 - end of helix removed outlier: 5.314A pdb=" N LEU U 65 " --> pdb=" O LEU U 61 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL U 66 " --> pdb=" O PRO U 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 47 removed outlier: 4.129A pdb=" N GLY V 13 " --> pdb=" O GLY V 9 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE V 37 " --> pdb=" O ALA V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 78 Proline residue: V 62 - end of helix removed outlier: 5.856A pdb=" N LEU V 65 " --> pdb=" O LEU V 61 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL V 66 " --> pdb=" O PRO V 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 47 removed outlier: 4.074A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 79 removed outlier: 4.458A pdb=" N GLY W 53 " --> pdb=" O SER W 50 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR W 54 " --> pdb=" O ASN W 51 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU W 61 " --> pdb=" O PHE W 58 " (cutoff:3.500A) Proline residue: W 62 - end of helix removed outlier: 3.583A pdb=" N LEU W 65 " --> pdb=" O PRO W 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 47 removed outlier: 3.724A pdb=" N ALA X 16 " --> pdb=" O ARG X 12 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 79 removed outlier: 3.778A pdb=" N PHE X 52 " --> pdb=" O ARG X 49 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLY X 53 " --> pdb=" O SER X 50 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR X 54 " --> pdb=" O ASN X 51 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU X 61 " --> pdb=" O PHE X 58 " (cutoff:3.500A) Proline residue: X 62 - end of helix removed outlier: 3.790A pdb=" N LEU X 65 " --> pdb=" O PRO X 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 47 removed outlier: 4.032A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 79 Proline residue: Y 62 - end of helix removed outlier: 6.031A pdb=" N LEU Y 65 " --> pdb=" O LEU Y 61 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL Y 66 " --> pdb=" O PRO Y 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 47 removed outlier: 3.807A pdb=" N GLY Z 13 " --> pdb=" O GLY Z 9 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 60 Processing helix chain 'Z' and resid 64 through 79 Processing sheet with id= A, first strand: chain 'A' and resid 63 through 65 removed outlier: 6.555A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 Processing sheet with id= C, first strand: chain 'A' and resid 82 through 84 removed outlier: 3.948A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N VAL A 251 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA A 321 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL A 253 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET A 323 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS A 255 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ASP A 325 " --> pdb=" O CYS A 255 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL A 381 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 117 through 119 Processing sheet with id= E, first strand: chain 'A' and resid 134 through 140 removed outlier: 6.921A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.809A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 37 through 40 removed outlier: 5.664A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 72 through 75 Processing sheet with id= I, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.913A pdb=" N GLY B 82 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 250 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE B 288 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR B 252 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N VAL B 320 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA B 377 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU B 322 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR B 379 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ALA B 324 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 137 through 139 Processing sheet with id= K, first strand: chain 'C' and resid 63 through 65 removed outlier: 6.659A pdb=" N ILE C 15 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE C 9 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 27 through 30 Processing sheet with id= M, first strand: chain 'C' and resid 72 through 75 Processing sheet with id= N, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.683A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 249 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA C 405 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 117 through 119 removed outlier: 3.662A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 366 through 369 Processing sheet with id= Q, first strand: chain 'C' and resid 134 through 138 removed outlier: 6.698A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.825A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 11 through 15 removed outlier: 4.580A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 81 through 84 Processing sheet with id= U, first strand: chain 'D' and resid 92 through 94 removed outlier: 8.756A pdb=" N PHE D 93 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU D 219 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE D 152 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.539A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL E 56 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 81 through 84 Processing sheet with id= X, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= Y, first strand: chain 'E' and resid 217 through 219 removed outlier: 6.556A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA E 188 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.596A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE F 32 " --> pdb=" O VAL F 76 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 81 through 84 Processing sheet with id= AB, first strand: chain 'F' and resid 129 through 131 removed outlier: 4.656A pdb=" N GLN F 129 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AD, first strand: chain 'F' and resid 307 through 312 removed outlier: 6.697A pdb=" N VAL F 218 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ALA F 193 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE F 220 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY F 195 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASN F 222 " --> pdb=" O GLY F 195 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 90 through 96 Processing sheet with id= AF, first strand: chain 'H' and resid 2 through 4 removed outlier: 5.972A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 141 through 144 Processing sheet with id= AH, first strand: chain 'L' and resid 141 through 144 Processing sheet with id= AI, first strand: chain 'N' and resid 304 through 306 removed outlier: 4.371A pdb=" N LEU N 279 " --> pdb=" O GLU N 33 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 140 through 145 Processing sheet with id= AK, first strand: chain 'N' and resid 389 through 391 2367 hydrogen bonds defined for protein. 6480 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: 15.18 Time building geometry restraints manager: 15.90 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: 10592 1.33 - 1.45: 6507 1.45 - 1.57: 23424 1.57 - 1.69: 8 1.69 - 1.80: 194 Bond restraints: 40725 Sorted by residual: bond pdb=" C LEU J 94 " pdb=" N PRO J 95 " ideal model delta sigma weight residual 1.335 1.386 -0.051 1.38e-02 5.25e+03 1.36e+01 bond pdb=" C LEU L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.21e+00 bond pdb=" CB ASP B 152 " pdb=" CG ASP B 152 " ideal model delta sigma weight residual 1.516 1.571 -0.055 2.50e-02 1.60e+03 4.88e+00 bond pdb=" CG LEU C 322 " pdb=" CD1 LEU C 322 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.95e+00 bond pdb=" CA ASP H 85 " pdb=" CB ASP H 85 " ideal model delta sigma weight residual 1.527 1.559 -0.032 1.61e-02 3.86e+03 3.86e+00 ... (remaining 40720 not shown) Histogram of bond angle deviations from ideal: 95.80 - 103.85: 610 103.85 - 111.91: 18874 111.91 - 119.97: 17298 119.97 - 128.03: 18367 128.03 - 136.08: 217 Bond angle restraints: 55366 Sorted by residual: angle pdb=" N VAL B 265 " pdb=" CA VAL B 265 " pdb=" C VAL B 265 " ideal model delta sigma weight residual 112.96 106.23 6.73 1.00e+00 1.00e+00 4.53e+01 angle pdb=" N GLY A 366 " pdb=" CA GLY A 366 " pdb=" C GLY A 366 " ideal model delta sigma weight residual 113.18 128.17 -14.99 2.37e+00 1.78e-01 4.00e+01 angle pdb=" C PRO B 151 " pdb=" N ASP B 152 " pdb=" CA ASP B 152 " ideal model delta sigma weight residual 124.82 134.57 -9.75 1.78e+00 3.16e-01 3.00e+01 angle pdb=" C GLU E 22 " pdb=" N ASN E 23 " pdb=" CA ASN E 23 " ideal model delta sigma weight residual 121.54 131.42 -9.88 1.91e+00 2.74e-01 2.68e+01 angle pdb=" CA ASP H 85 " pdb=" CB ASP H 85 " pdb=" CG ASP H 85 " ideal model delta sigma weight residual 112.60 117.54 -4.94 1.00e+00 1.00e+00 2.44e+01 ... (remaining 55361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.56: 24168 29.56 - 59.11: 309 59.11 - 88.67: 5 88.67 - 118.22: 1 118.22 - 147.78: 1 Dihedral angle restraints: 24484 sinusoidal: 7993 harmonic: 16491 Sorted by residual: dihedral pdb=" C5' ADP A 602 " pdb=" O5' ADP A 602 " pdb=" PA ADP A 602 " pdb=" O2A ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 87.78 -147.78 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" CA MET A 294 " pdb=" C MET A 294 " pdb=" N PRO A 295 " pdb=" CA PRO A 295 " ideal model delta harmonic sigma weight residual -180.00 -150.40 -29.60 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA GLU F 182 " pdb=" C GLU F 182 " pdb=" N LYS F 183 " pdb=" CA LYS F 183 " ideal model delta harmonic sigma weight residual 180.00 150.76 29.24 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 24481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 5619 0.084 - 0.168: 745 0.168 - 0.252: 49 0.252 - 0.337: 4 0.337 - 0.421: 2 Chirality restraints: 6419 Sorted by residual: chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CB VAL B 378 " pdb=" CA VAL B 378 " pdb=" CG1 VAL B 378 " pdb=" CG2 VAL B 378 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA ASP F 259 " pdb=" N ASP F 259 " pdb=" C ASP F 259 " pdb=" CB ASP F 259 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 6416 not shown) Planarity restraints: 7462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 234 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C LYS C 234 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS C 234 " -0.022 2.00e-02 2.50e+03 pdb=" N THR C 235 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 198 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" C GLN F 198 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN F 198 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG F 199 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 226 " 0.047 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO C 227 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 227 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 227 " 0.039 5.00e-02 4.00e+02 ... (remaining 7459 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1224 2.70 - 3.25: 38672 3.25 - 3.80: 64412 3.80 - 4.35: 76356 4.35 - 4.90: 130499 Nonbonded interactions: 311163 Sorted by model distance: nonbonded pdb="MG MG A 601 " pdb=" O3B ADP A 602 " model vdw 2.152 2.170 nonbonded pdb=" OE2 GLU D 109 " pdb=" OH TYR D 244 " model vdw 2.195 2.440 nonbonded pdb=" OD1 ASP B 446 " pdb=" OH TYR B 513 " model vdw 2.276 2.440 nonbonded pdb=" O PRO C 386 " pdb=" OH TYR E 331 " model vdw 2.276 2.440 nonbonded pdb=" OE1 GLU A 38 " pdb=" OH TYR A 52 " model vdw 2.278 2.440 ... (remaining 311158 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' and resid 1 through 577) selection = (chain 'B' and resid 1 through 577) selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 5 through 464) selection = (chain 'F' and resid 5 through 464) } ncs_group { reference = (chain 'I' and resid 22 through 120) selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } ncs_group { reference = (chain 'O' and resid 9 through 80) selection = (chain 'P' and resid 9 through 80) selection = (chain 'Q' and resid 9 through 80) selection = (chain 'R' and resid 9 through 80) selection = (chain 'S' and resid 9 through 80) selection = (chain 'T' and resid 9 through 80) selection = (chain 'U' and resid 9 through 80) selection = (chain 'V' and resid 9 through 80) selection = (chain 'W' and resid 9 through 80) selection = chain 'X' selection = (chain 'Y' and resid 9 through 80) selection = (chain 'Z' and resid 9 through 80) } 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: 0.360 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: 0.030 Extract box with map and model: 3.400 Check model and map are aligned: 0.580 Set scattering table: 0.350 Process input model: 102.420 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.240 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.007 0.091 40725 Z= 0.442 Angle : 0.973 16.106 55366 Z= 0.526 Chirality : 0.057 0.421 6419 Planarity : 0.007 0.071 7462 Dihedral : 9.782 147.776 13946 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.21 % Favored : 93.75 % Rotamer: Outliers : 0.19 % Allowed : 4.41 % Favored : 95.40 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.08), residues: 5795 helix: -2.14 (0.06), residues: 3121 sheet: -2.46 (0.19), residues: 600 loop : -3.07 (0.12), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 438 HIS 0.009 0.003 HIS F 323 PHE 0.031 0.003 PHE D 204 TYR 0.029 0.003 TYR D 411 ARG 0.018 0.001 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1050 time to evaluate : 4.074 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 TARDY: cannot create tardy model for: "PRO L 146 " (corrupted residue). Skipping it. Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable