Starting phenix.real_space_refine on Sat Dec 9 08:13:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bk4_9400/12_2023/5bk4_9400_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bk4_9400/12_2023/5bk4_9400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bk4_9400/12_2023/5bk4_9400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bk4_9400/12_2023/5bk4_9400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bk4_9400/12_2023/5bk4_9400_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bk4_9400/12_2023/5bk4_9400_updated.pdb" } resolution = 3.9 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= 0.002 sd= 0.009 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 136 5.49 5 S 268 5.16 5 C 38860 2.51 5 N 10966 2.21 5 O 12252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ARG 224": "NH1" <-> "NH2" Residue "2 ARG 319": "NH1" <-> "NH2" Residue "2 ARG 459": "NH1" <-> "NH2" Residue "2 PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 489": "NH1" <-> "NH2" Residue "2 ARG 509": "NH1" <-> "NH2" Residue "2 ARG 534": "NH1" <-> "NH2" Residue "2 ARG 656": "NH1" <-> "NH2" Residue "2 ARG 705": "NH1" <-> "NH2" Residue "2 ARG 794": "NH1" <-> "NH2" Residue "2 ARG 808": "NH1" <-> "NH2" Residue "2 ARG 824": "NH1" <-> "NH2" Residue "2 ARG 854": "NH1" <-> "NH2" Residue "2 ARG 859": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 104": "NH1" <-> "NH2" Residue "3 ARG 108": "NH1" <-> "NH2" Residue "3 ARG 208": "NH1" <-> "NH2" Residue "3 ARG 224": "NH1" <-> "NH2" Residue "3 ARG 291": "NH1" <-> "NH2" Residue "3 ARG 420": "NH1" <-> "NH2" Residue "3 ARG 435": "NH1" <-> "NH2" Residue "3 ARG 483": "NH1" <-> "NH2" Residue "3 ARG 557": "NH1" <-> "NH2" Residue "3 ARG 657": "NH1" <-> "NH2" Residue "3 ARG 700": "NH1" <-> "NH2" Residue "3 ARG 734": "NH1" <-> "NH2" Residue "4 ARG 178": "NH1" <-> "NH2" Residue "4 ARG 234": "NH1" <-> "NH2" Residue "4 ARG 373": "NH1" <-> "NH2" Residue "4 ARG 388": "NH1" <-> "NH2" Residue "4 ARG 428": "NH1" <-> "NH2" Residue "4 TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 499": "NH1" <-> "NH2" Residue "4 ARG 557": "NH1" <-> "NH2" Residue "4 ARG 559": "NH1" <-> "NH2" Residue "4 ARG 607": "NH1" <-> "NH2" Residue "4 ARG 681": "NH1" <-> "NH2" Residue "4 ARG 796": "NH1" <-> "NH2" Residue "4 ARG 827": "NH1" <-> "NH2" Residue "5 TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 106": "NH1" <-> "NH2" Residue "5 ARG 407": "NH1" <-> "NH2" Residue "5 ARG 455": "NH1" <-> "NH2" Residue "5 ARG 460": "NH1" <-> "NH2" Residue "5 PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 651": "NH1" <-> "NH2" Residue "6 ARG 137": "NH1" <-> "NH2" Residue "6 ARG 176": "NH1" <-> "NH2" Residue "6 ARG 190": "NH1" <-> "NH2" Residue "6 ARG 277": "NH1" <-> "NH2" Residue "6 ARG 280": "NH1" <-> "NH2" Residue "6 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 360": "NH1" <-> "NH2" Residue "6 ARG 375": "NH1" <-> "NH2" Residue "6 ARG 382": "NH1" <-> "NH2" Residue "6 ARG 424": "NH1" <-> "NH2" Residue "6 ARG 446": "NH1" <-> "NH2" Residue "6 ARG 531": "NH1" <-> "NH2" Residue "6 ARG 566": "NH1" <-> "NH2" Residue "6 ARG 594": "NH1" <-> "NH2" Residue "6 TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 691": "NH1" <-> "NH2" Residue "6 ARG 708": "NH1" <-> "NH2" Residue "6 ARG 781": "NH1" <-> "NH2" Residue "6 ARG 790": "NH1" <-> "NH2" Residue "7 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 152": "NH1" <-> "NH2" Residue "7 ARG 199": "NH1" <-> "NH2" Residue "7 TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 213": "NH1" <-> "NH2" Residue "7 ARG 214": "NH1" <-> "NH2" Residue "7 ARG 216": "NH1" <-> "NH2" Residue "7 PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 451": "NH1" <-> "NH2" Residue "7 ARG 573": "NH1" <-> "NH2" Residue "7 ARG 577": "NH1" <-> "NH2" Residue "7 ARG 606": "NH1" <-> "NH2" Residue "7 ARG 694": "NH1" <-> "NH2" Residue "7 ARG 703": "NH1" <-> "NH2" Residue "7 ARG 718": "NH1" <-> "NH2" Residue "A ARG 224": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ARG 534": "NH1" <-> "NH2" Residue "A ARG 656": "NH1" <-> "NH2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "A ARG 794": "NH1" <-> "NH2" Residue "A ARG 808": "NH1" <-> "NH2" Residue "A ARG 824": "NH1" <-> "NH2" Residue "A ARG 854": "NH1" <-> "NH2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 435": "NH1" <-> "NH2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 657": "NH1" <-> "NH2" Residue "B ARG 700": "NH1" <-> "NH2" Residue "B ARG 734": "NH1" <-> "NH2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C ARG 373": "NH1" <-> "NH2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C ARG 428": "NH1" <-> "NH2" Residue "C TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C ARG 559": "NH1" <-> "NH2" Residue "C ARG 607": "NH1" <-> "NH2" Residue "C ARG 681": "NH1" <-> "NH2" Residue "C ARG 796": "NH1" <-> "NH2" Residue "C ARG 827": "NH1" <-> "NH2" Residue "D TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D ARG 455": "NH1" <-> "NH2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 651": "NH1" <-> "NH2" Residue "E ARG 137": "NH1" <-> "NH2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E ARG 277": "NH1" <-> "NH2" Residue "E ARG 280": "NH1" <-> "NH2" Residue "E TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 360": "NH1" <-> "NH2" Residue "E ARG 375": "NH1" <-> "NH2" Residue "E ARG 382": "NH1" <-> "NH2" Residue "E ARG 424": "NH1" <-> "NH2" Residue "E ARG 446": "NH1" <-> "NH2" Residue "E ARG 531": "NH1" <-> "NH2" Residue "E ARG 566": "NH1" <-> "NH2" Residue "E ARG 594": "NH1" <-> "NH2" Residue "E TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 691": "NH1" <-> "NH2" Residue "E ARG 708": "NH1" <-> "NH2" Residue "E ARG 781": "NH1" <-> "NH2" Residue "E ARG 790": "NH1" <-> "NH2" Residue "F PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "F ARG 214": "NH1" <-> "NH2" Residue "F ARG 216": "NH1" <-> "NH2" Residue "F PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 451": "NH1" <-> "NH2" Residue "F ARG 573": "NH1" <-> "NH2" Residue "F ARG 577": "NH1" <-> "NH2" Residue "F ARG 606": "NH1" <-> "NH2" Residue "F ARG 694": "NH1" <-> "NH2" Residue "F ARG 703": "NH1" <-> "NH2" Residue "F ARG 718": "NH1" <-> "NH2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 62482 Number of models: 1 Model: "" Number of chains: 22 Chain: "2" Number of atoms: 4714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4714 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 14, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 565} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "3" Number of atoms: 4734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4734 Classifications: {'peptide': 604} Link IDs: {'CIS': 11, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 568} Chain breaks: 3 Chain: "4" Number of atoms: 5127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5127 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 10, 'PTRANS': 23, 'TRANS': 612} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "5" Number of atoms: 5165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5165 Classifications: {'peptide': 661} Link IDs: {'CIS': 17, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 616} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4731 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'CIS': 25, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 567} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 92 Chain: "7" Number of atoms: 5432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5432 Classifications: {'peptide': 689} Link IDs: {'CIS': 12, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 646} Chain breaks: 3 Chain: "A" Number of atoms: 4714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4714 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 14, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 565} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 4734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4734 Classifications: {'peptide': 604} Link IDs: {'CIS': 11, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 568} Chain breaks: 3 Chain: "C" Number of atoms: 5127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5127 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 10, 'PTRANS': 23, 'TRANS': 612} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 5165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5165 Classifications: {'peptide': 661} Link IDs: {'CIS': 17, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 616} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4731 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'CIS': 25, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 567} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 92 Chain: "F" Number of atoms: 5432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5432 Classifications: {'peptide': 689} Link IDs: {'CIS': 12, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 646} Chain breaks: 3 Chain: "S" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1230 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain: "O" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1230 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain: "2" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.56, per 1000 atoms: 0.41 Number of scatterers: 62482 At special positions: 0 Unit cell: (163.2, 223.04, 154.496, 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 268 16.00 P 136 15.00 O 12252 8.00 N 10966 7.00 C 38860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS 5 183 " - pdb=" SG CYS 5 211 " distance=2.04 Simple disulfide: pdb=" SG CYS 5 183 " - pdb=" SG CYS 5 236 " distance=2.04 Simple disulfide: pdb=" SG CYS 5 186 " - pdb=" SG CYS 5 211 " distance=2.02 Simple disulfide: pdb=" SG CYS 5 186 " - pdb=" SG CYS 5 236 " distance=2.02 Simple disulfide: pdb=" SG CYS 5 211 " - pdb=" SG CYS 5 236 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 265 " - pdb=" SG CYS 7 289 " distance=2.02 Simple disulfide: pdb=" SG CYS 7 474 " - pdb=" SG CYS 7 522 " distance=2.04 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 211 " distance=2.04 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 236 " distance=2.04 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 211 " distance=2.02 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 236 " distance=2.02 Simple disulfide: pdb=" SG CYS D 211 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 265 " - pdb=" SG CYS F 289 " distance=2.02 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 522 " distance=2.04 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: 17.34 Conformation dependent library (CDL) restraints added in 7.8 seconds 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14508 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 248 helices and 86 sheets defined 33.0% alpha, 8.3% beta 57 base pairs and 113 stacking pairs defined. Time for finding SS restraints: 19.28 Creating SS restraints... Processing helix chain '2' and resid 202 through 215 removed outlier: 3.707A pdb=" N ARG 2 205 " --> pdb=" O ASN 2 202 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS 2 212 " --> pdb=" O ARG 2 209 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU 2 215 " --> pdb=" O LYS 2 212 " (cutoff:3.500A) Processing helix chain '2' and resid 226 through 233 Processing helix chain '2' and resid 246 through 252 Processing helix chain '2' and resid 254 through 261 Processing helix chain '2' and resid 264 through 282 removed outlier: 4.627A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL 2 274 " --> pdb=" O ILE 2 270 " (cutoff:3.500A) Processing helix chain '2' and resid 311 through 313 No H-bonds generated for 'chain '2' and resid 311 through 313' Processing helix chain '2' and resid 412 through 414 No H-bonds generated for 'chain '2' and resid 412 through 414' Processing helix chain '2' and resid 478 through 482 Processing helix chain '2' and resid 484 through 489 removed outlier: 3.850A pdb=" N SER 2 488 " --> pdb=" O PHE 2 484 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG 2 489 " --> pdb=" O ARG 2 485 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 484 through 489' Processing helix chain '2' and resid 493 through 499 Processing helix chain '2' and resid 509 through 520 Processing helix chain '2' and resid 548 through 559 removed outlier: 3.951A pdb=" N LEU 2 553 " --> pdb=" O SER 2 550 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS 2 554 " --> pdb=" O GLN 2 551 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU 2 557 " --> pdb=" O LYS 2 554 " (cutoff:3.500A) Processing helix chain '2' and resid 595 through 598 No H-bonds generated for 'chain '2' and resid 595 through 598' Processing helix chain '2' and resid 609 through 611 No H-bonds generated for 'chain '2' and resid 609 through 611' Processing helix chain '2' and resid 614 through 625 removed outlier: 3.693A pdb=" N SER 2 619 " --> pdb=" O GLN 2 615 " (cutoff:3.500A) Processing helix chain '2' and resid 663 through 666 No H-bonds generated for 'chain '2' and resid 663 through 666' Processing helix chain '2' and resid 689 through 703 removed outlier: 3.659A pdb=" N PHE 2 698 " --> pdb=" O ARG 2 694 " (cutoff:3.500A) Processing helix chain '2' and resid 760 through 773 removed outlier: 3.667A pdb=" N HIS 2 768 " --> pdb=" O MET 2 764 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS 2 773 " --> pdb=" O TYR 2 769 " (cutoff:3.500A) Processing helix chain '2' and resid 784 through 796 removed outlier: 4.002A pdb=" N ARG 2 788 " --> pdb=" O ASP 2 784 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU 2 796 " --> pdb=" O ASP 2 792 " (cutoff:3.500A) Processing helix chain '2' and resid 808 through 822 removed outlier: 4.193A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) Processing helix chain '2' and resid 831 through 847 Processing helix chain '2' and resid 851 through 858 removed outlier: 3.525A pdb=" N ARG 2 854 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG 2 855 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG 2 858 " --> pdb=" O ARG 2 855 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 34 Processing helix chain '3' and resid 37 through 58 Processing helix chain '3' and resid 108 through 114 Processing helix chain '3' and resid 118 through 120 No H-bonds generated for 'chain '3' and resid 118 through 120' Processing helix chain '3' and resid 122 through 136 Processing helix chain '3' and resid 280 through 282 No H-bonds generated for 'chain '3' and resid 280 through 282' Processing helix chain '3' and resid 344 through 355 removed outlier: 4.374A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) Processing helix chain '3' and resid 359 through 366 removed outlier: 3.848A pdb=" N GLN 3 365 " --> pdb=" O ASP 3 361 " (cutoff:3.500A) Processing helix chain '3' and resid 375 through 386 Processing helix chain '3' and resid 415 through 425 removed outlier: 4.157A pdb=" N LEU 3 419 " --> pdb=" O LYS 3 415 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG 3 420 " --> pdb=" O SER 3 416 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE 3 421 " --> pdb=" O GLN 3 417 " (cutoff:3.500A) Processing helix chain '3' and resid 475 through 477 No H-bonds generated for 'chain '3' and resid 475 through 477' Processing helix chain '3' and resid 480 through 490 removed outlier: 3.941A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) Processing helix chain '3' and resid 538 through 542 Processing helix chain '3' and resid 556 through 569 removed outlier: 3.784A pdb=" N HIS 3 564 " --> pdb=" O SER 3 560 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS 3 569 " --> pdb=" O VAL 3 565 " (cutoff:3.500A) Processing helix chain '3' and resid 653 through 665 removed outlier: 4.445A pdb=" N LYS 3 658 " --> pdb=" O PRO 3 654 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR 3 662 " --> pdb=" O LYS 3 658 " (cutoff:3.500A) Processing helix chain '3' and resid 673 through 693 removed outlier: 3.540A pdb=" N ILE 3 676 " --> pdb=" O GLN 3 673 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASN 3 677 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL 3 678 " --> pdb=" O ALA 3 675 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL 3 680 " --> pdb=" O ASN 3 677 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS 3 681 " --> pdb=" O VAL 3 678 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN 3 682 " --> pdb=" O ILE 3 679 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR 3 684 " --> pdb=" O LYS 3 681 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG 3 687 " --> pdb=" O THR 3 684 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP 3 689 " --> pdb=" O LEU 3 686 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP 3 690 " --> pdb=" O ARG 3 687 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASN 3 691 " --> pdb=" O ASN 3 688 " (cutoff:3.500A) Processing helix chain '3' and resid 699 through 715 Processing helix chain '3' and resid 723 through 737 Processing helix chain '4' and resid 187 through 197 Processing helix chain '4' and resid 204 through 209 Processing helix chain '4' and resid 225 through 235 Processing helix chain '4' and resid 246 through 250 Processing helix chain '4' and resid 256 through 263 removed outlier: 3.779A pdb=" N ASN 4 263 " --> pdb=" O HIS 4 259 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 286 removed outlier: 3.711A pdb=" N VAL 4 285 " --> pdb=" O VAL 4 281 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASP 4 286 " --> pdb=" O SER 4 282 " (cutoff:3.500A) Processing helix chain '4' and resid 293 through 298 removed outlier: 3.503A pdb=" N GLU 4 297 " --> pdb=" O LEU 4 293 " (cutoff:3.500A) Processing helix chain '4' and resid 421 through 423 No H-bonds generated for 'chain '4' and resid 421 through 423' Processing helix chain '4' and resid 482 through 487 Processing helix chain '4' and resid 504 through 514 removed outlier: 3.944A pdb=" N LYS 4 508 " --> pdb=" O GLN 4 504 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA 4 514 " --> pdb=" O ARG 4 510 " (cutoff:3.500A) Processing helix chain '4' and resid 516 through 524 removed outlier: 4.448A pdb=" N TYR 4 519 " --> pdb=" O GLU 4 516 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU 4 522 " --> pdb=" O TYR 4 519 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA 4 523 " --> pdb=" O SER 4 520 " (cutoff:3.500A) Processing helix chain '4' and resid 534 through 543 Processing helix chain '4' and resid 574 through 584 Processing helix chain '4' and resid 599 through 601 No H-bonds generated for 'chain '4' and resid 599 through 601' Processing helix chain '4' and resid 634 through 636 No H-bonds generated for 'chain '4' and resid 634 through 636' Processing helix chain '4' and resid 645 through 648 No H-bonds generated for 'chain '4' and resid 645 through 648' Processing helix chain '4' and resid 696 through 701 Processing helix chain '4' and resid 715 through 731 removed outlier: 4.407A pdb=" N GLU 4 719 " --> pdb=" O LYS 4 715 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLU 4 730 " --> pdb=" O ASN 4 726 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASP 4 731 " --> pdb=" O LEU 4 727 " (cutoff:3.500A) Processing helix chain '4' and resid 746 through 756 Processing helix chain '4' and resid 764 through 778 removed outlier: 4.705A pdb=" N THR 4 768 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU 4 770 " --> pdb=" O LYS 4 767 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL 4 771 " --> pdb=" O THR 4 768 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG 4 772 " --> pdb=" O GLU 4 769 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL 4 775 " --> pdb=" O ARG 4 772 " (cutoff:3.500A) Processing helix chain '4' and resid 795 through 810 Processing helix chain '4' and resid 822 through 836 removed outlier: 4.590A pdb=" N ILE 4 829 " --> pdb=" O ALA 4 825 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA 4 832 " --> pdb=" O LEU 4 828 " (cutoff:3.500A) Processing helix chain '5' and resid 28 through 35 Processing helix chain '5' and resid 46 through 55 removed outlier: 4.367A pdb=" N LEU 5 55 " --> pdb=" O ARG 5 51 " (cutoff:3.500A) Processing helix chain '5' and resid 65 through 71 Processing helix chain '5' and resid 74 through 81 Processing helix chain '5' and resid 83 through 85 No H-bonds generated for 'chain '5' and resid 83 through 85' Processing helix chain '5' and resid 87 through 107 removed outlier: 3.977A pdb=" N VAL 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 153 through 155 No H-bonds generated for 'chain '5' and resid 153 through 155' Processing helix chain '5' and resid 220 through 224 Processing helix chain '5' and resid 352 through 360 Processing helix chain '5' and resid 366 through 370 Processing helix chain '5' and resid 382 through 387 Processing helix chain '5' and resid 422 through 432 Processing helix chain '5' and resid 490 through 496 Processing helix chain '5' and resid 528 through 533 Processing helix chain '5' and resid 546 through 549 No H-bonds generated for 'chain '5' and resid 546 through 549' Processing helix chain '5' and resid 562 through 576 Processing helix chain '5' and resid 580 through 589 Processing helix chain '5' and resid 597 through 608 removed outlier: 3.943A pdb=" N ARG 5 601 " --> pdb=" O GLU 5 597 " (cutoff:3.500A) Processing helix chain '5' and resid 616 through 639 removed outlier: 4.374A pdb=" N THR 5 628 " --> pdb=" O SER 5 624 " (cutoff:3.500A) Processing helix chain '5' and resid 650 through 667 removed outlier: 3.831A pdb=" N THR 5 660 " --> pdb=" O ILE 5 656 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU 5 661 " --> pdb=" O ILE 5 657 " (cutoff:3.500A) Processing helix chain '5' and resid 675 through 692 removed outlier: 4.711A pdb=" N ALA 5 680 " --> pdb=" O HIS 5 676 " (cutoff:3.500A) Processing helix chain '6' and resid 104 through 120 Processing helix chain '6' and resid 136 through 146 removed outlier: 3.764A pdb=" N TYR 6 146 " --> pdb=" O PHE 6 142 " (cutoff:3.500A) Processing helix chain '6' and resid 156 through 161 removed outlier: 3.589A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) Processing helix chain '6' and resid 167 through 170 No H-bonds generated for 'chain '6' and resid 167 through 170' Processing helix chain '6' and resid 175 through 192 removed outlier: 4.065A pdb=" N LEU 6 178 " --> pdb=" O TYR 6 175 " (cutoff:3.500A) Proline residue: 6 179 - end of helix removed outlier: 3.760A pdb=" N GLN 6 182 " --> pdb=" O PRO 6 179 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU 6 185 " --> pdb=" O GLN 6 182 " (cutoff:3.500A) Processing helix chain '6' and resid 383 through 385 No H-bonds generated for 'chain '6' and resid 383 through 385' Processing helix chain '6' and resid 513 through 520 Processing helix chain '6' and resid 525 through 530 Processing helix chain '6' and resid 542 through 550 Processing helix chain '6' and resid 582 through 591 Processing helix chain '6' and resid 646 through 657 Processing helix chain '6' and resid 696 through 698 No H-bonds generated for 'chain '6' and resid 696 through 698' Processing helix chain '6' and resid 721 through 734 Processing helix chain '6' and resid 748 through 760 removed outlier: 3.967A pdb=" N ARG 6 752 " --> pdb=" O ALA 6 748 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS 6 756 " --> pdb=" O ARG 6 752 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) Processing helix chain '6' and resid 768 through 783 removed outlier: 3.732A pdb=" N GLU 6 775 " --> pdb=" O TYR 6 772 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS 6 776 " --> pdb=" O LEU 6 773 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS 6 782 " --> pdb=" O GLU 6 779 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP 6 783 " --> pdb=" O LEU 6 780 " (cutoff:3.500A) Processing helix chain '6' and resid 797 through 813 removed outlier: 3.885A pdb=" N ILE 6 804 " --> pdb=" O LEU 6 800 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG 6 805 " --> pdb=" O GLU 6 801 " (cutoff:3.500A) Processing helix chain '6' and resid 821 through 839 removed outlier: 3.746A pdb=" N VAL 6 838 " --> pdb=" O SER 6 834 " (cutoff:3.500A) Processing helix chain '7' and resid 16 through 26 Processing helix chain '7' and resid 63 through 71 Processing helix chain '7' and resid 84 through 95 Processing helix chain '7' and resid 103 through 108 Processing helix chain '7' and resid 112 through 121 Processing helix chain '7' and resid 139 through 163 removed outlier: 3.907A pdb=" N ARG 7 157 " --> pdb=" O MET 7 153 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR 7 158 " --> pdb=" O LEU 7 154 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG 7 162 " --> pdb=" O THR 7 158 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N SER 7 163 " --> pdb=" O ASN 7 159 " (cutoff:3.500A) Processing helix chain '7' and resid 179 through 187 removed outlier: 3.874A pdb=" N ASP 7 187 " --> pdb=" O GLU 7 183 " (cutoff:3.500A) Processing helix chain '7' and resid 209 through 215 removed outlier: 3.516A pdb=" N TYR 7 215 " --> pdb=" O CYS 7 211 " (cutoff:3.500A) Processing helix chain '7' and resid 337 through 339 No H-bonds generated for 'chain '7' and resid 337 through 339' Processing helix chain '7' and resid 364 through 366 No H-bonds generated for 'chain '7' and resid 364 through 366' Processing helix chain '7' and resid 397 through 407 removed outlier: 3.571A pdb=" N VAL 7 401 " --> pdb=" O GLU 7 398 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N MET 7 402 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU 7 403 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE 7 405 " --> pdb=" O MET 7 402 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR 7 406 " --> pdb=" O GLU 7 403 " (cutoff:3.500A) Processing helix chain '7' and resid 410 through 417 Processing helix chain '7' and resid 426 through 437 removed outlier: 3.772A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) Processing helix chain '7' and resid 467 through 476 Processing helix chain '7' and resid 490 through 493 No H-bonds generated for 'chain '7' and resid 490 through 493' Processing helix chain '7' and resid 512 through 515 No H-bonds generated for 'chain '7' and resid 512 through 515' Processing helix chain '7' and resid 526 through 528 No H-bonds generated for 'chain '7' and resid 526 through 528' Processing helix chain '7' and resid 531 through 541 Processing helix chain '7' and resid 588 through 593 Processing helix chain '7' and resid 607 through 621 removed outlier: 3.824A pdb=" N GLU 7 610 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU 7 614 " --> pdb=" O LYS 7 611 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR 7 617 " --> pdb=" O GLU 7 614 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET 7 621 " --> pdb=" O TYR 7 618 " (cutoff:3.500A) Processing helix chain '7' and resid 635 through 645 Processing helix chain '7' and resid 655 through 671 Processing helix chain '7' and resid 686 through 702 removed outlier: 3.912A pdb=" N LYS 7 701 " --> pdb=" O GLN 7 697 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU 7 702 " --> pdb=" O ALA 7 698 " (cutoff:3.500A) Processing helix chain '7' and resid 710 through 723 Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.708A pdb=" N ARG A 205 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 212 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 215 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 246 through 252 Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 264 through 282 removed outlier: 4.627A pdb=" N LEU A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.851A pdb=" N SER A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 489' Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 509 through 520 Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.951A pdb=" N LEU A 553 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 554 " --> pdb=" O GLN A 551 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 557 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 598 No H-bonds generated for 'chain 'A' and resid 595 through 598' Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 614 through 625 removed outlier: 3.693A pdb=" N SER A 619 " --> pdb=" O GLN A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 666 No H-bonds generated for 'chain 'A' and resid 663 through 666' Processing helix chain 'A' and resid 689 through 703 removed outlier: 3.659A pdb=" N PHE A 698 " --> pdb=" O ARG A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 773 removed outlier: 3.668A pdb=" N HIS A 768 " --> pdb=" O MET A 764 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A 773 " --> pdb=" O TYR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 796 removed outlier: 4.002A pdb=" N ARG A 788 " --> pdb=" O ASP A 784 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 822 removed outlier: 4.193A pdb=" N ILE A 813 " --> pdb=" O HIS A 809 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 847 Processing helix chain 'A' and resid 851 through 858 removed outlier: 3.525A pdb=" N ARG A 854 " --> pdb=" O VAL A 851 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 855 " --> pdb=" O SER A 852 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 858 " --> pdb=" O ARG A 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 34 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 122 through 136 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 344 through 355 removed outlier: 4.373A pdb=" N LYS B 355 " --> pdb=" O ASN B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.848A pdb=" N GLN B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 386 Processing helix chain 'B' and resid 415 through 425 removed outlier: 4.156A pdb=" N LEU B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'B' and resid 480 through 490 removed outlier: 3.942A pdb=" N ALA B 485 " --> pdb=" O VAL B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.784A pdb=" N HIS B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS B 569 " --> pdb=" O VAL B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 665 removed outlier: 4.445A pdb=" N LYS B 658 " --> pdb=" O PRO B 654 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR B 662 " --> pdb=" O LYS B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 693 removed outlier: 3.540A pdb=" N ILE B 676 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASN B 677 " --> pdb=" O GLU B 674 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL B 678 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 680 " --> pdb=" O ASN B 677 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 681 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN B 682 " --> pdb=" O ILE B 679 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 684 " --> pdb=" O LYS B 681 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 687 " --> pdb=" O THR B 684 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP B 689 " --> pdb=" O LEU B 686 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP B 690 " --> pdb=" O ARG B 687 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ASN B 691 " --> pdb=" O ASN B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 715 Processing helix chain 'B' and resid 723 through 737 Processing helix chain 'C' and resid 187 through 197 Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 225 through 235 Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 256 through 263 removed outlier: 3.780A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 286 removed outlier: 3.711A pdb=" N VAL C 285 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASP C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 298 removed outlier: 3.502A pdb=" N GLU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 423 No H-bonds generated for 'chain 'C' and resid 421 through 423' Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 504 through 514 removed outlier: 3.945A pdb=" N LYS C 508 " --> pdb=" O GLN C 504 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA C 514 " --> pdb=" O ARG C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 524 removed outlier: 4.448A pdb=" N TYR C 519 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU C 522 " --> pdb=" O TYR C 519 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 523 " --> pdb=" O SER C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 543 Processing helix chain 'C' and resid 574 through 584 Processing helix chain 'C' and resid 599 through 601 No H-bonds generated for 'chain 'C' and resid 599 through 601' Processing helix chain 'C' and resid 634 through 636 No H-bonds generated for 'chain 'C' and resid 634 through 636' Processing helix chain 'C' and resid 645 through 648 No H-bonds generated for 'chain 'C' and resid 645 through 648' Processing helix chain 'C' and resid 696 through 701 Processing helix chain 'C' and resid 715 through 731 removed outlier: 4.407A pdb=" N GLU C 719 " --> pdb=" O LYS C 715 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLU C 730 " --> pdb=" O ASN C 726 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASP C 731 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 756 Processing helix chain 'C' and resid 764 through 778 removed outlier: 4.706A pdb=" N THR C 768 " --> pdb=" O ALA C 765 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 770 " --> pdb=" O LYS C 767 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 771 " --> pdb=" O THR C 768 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG C 772 " --> pdb=" O GLU C 769 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 775 " --> pdb=" O ARG C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 810 Processing helix chain 'C' and resid 822 through 836 removed outlier: 4.589A pdb=" N ILE C 829 " --> pdb=" O ALA C 825 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA C 832 " --> pdb=" O LEU C 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 35 Processing helix chain 'D' and resid 46 through 55 removed outlier: 4.367A pdb=" N LEU D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 71 Processing helix chain 'D' and resid 74 through 81 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 87 through 107 removed outlier: 3.978A pdb=" N VAL D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 220 through 224 Processing helix chain 'D' and resid 352 through 360 Processing helix chain 'D' and resid 366 through 370 Processing helix chain 'D' and resid 382 through 387 Processing helix chain 'D' and resid 422 through 432 Processing helix chain 'D' and resid 490 through 496 Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 546 through 549 No H-bonds generated for 'chain 'D' and resid 546 through 549' Processing helix chain 'D' and resid 562 through 576 Processing helix chain 'D' and resid 580 through 589 Processing helix chain 'D' and resid 597 through 608 removed outlier: 3.943A pdb=" N ARG D 601 " --> pdb=" O GLU D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 639 removed outlier: 4.374A pdb=" N THR D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 667 removed outlier: 3.831A pdb=" N THR D 660 " --> pdb=" O ILE D 656 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU D 661 " --> pdb=" O ILE D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 692 removed outlier: 4.711A pdb=" N ALA D 680 " --> pdb=" O HIS D 676 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 120 Processing helix chain 'E' and resid 136 through 146 removed outlier: 3.765A pdb=" N TYR E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 161 removed outlier: 3.589A pdb=" N ARG E 161 " --> pdb=" O HIS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 170 No H-bonds generated for 'chain 'E' and resid 167 through 170' Processing helix chain 'E' and resid 175 through 192 removed outlier: 4.064A pdb=" N LEU E 178 " --> pdb=" O TYR E 175 " (cutoff:3.500A) Proline residue: E 179 - end of helix removed outlier: 3.761A pdb=" N GLN E 182 " --> pdb=" O PRO E 179 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU E 185 " --> pdb=" O GLN E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 385 No H-bonds generated for 'chain 'E' and resid 383 through 385' Processing helix chain 'E' and resid 513 through 520 Processing helix chain 'E' and resid 525 through 530 Processing helix chain 'E' and resid 542 through 550 Processing helix chain 'E' and resid 582 through 591 Processing helix chain 'E' and resid 646 through 657 Processing helix chain 'E' and resid 696 through 698 No H-bonds generated for 'chain 'E' and resid 696 through 698' Processing helix chain 'E' and resid 721 through 734 Processing helix chain 'E' and resid 748 through 760 removed outlier: 3.968A pdb=" N ARG E 752 " --> pdb=" O ALA E 748 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS E 756 " --> pdb=" O ARG E 752 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR E 760 " --> pdb=" O LYS E 756 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 783 removed outlier: 3.733A pdb=" N GLU E 775 " --> pdb=" O TYR E 772 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS E 776 " --> pdb=" O LEU E 773 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS E 782 " --> pdb=" O GLU E 779 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP E 783 " --> pdb=" O LEU E 780 " (cutoff:3.500A) Processing helix chain 'E' and resid 797 through 813 removed outlier: 3.886A pdb=" N ILE E 804 " --> pdb=" O LEU E 800 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG E 805 " --> pdb=" O GLU E 801 " (cutoff:3.500A) Processing helix chain 'E' and resid 821 through 839 removed outlier: 3.747A pdb=" N VAL E 838 " --> pdb=" O SER E 834 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 26 Processing helix chain 'F' and resid 63 through 71 Processing helix chain 'F' and resid 84 through 95 Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 112 through 121 Processing helix chain 'F' and resid 139 through 163 removed outlier: 3.906A pdb=" N ARG F 157 " --> pdb=" O MET F 153 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG F 162 " --> pdb=" O THR F 158 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER F 163 " --> pdb=" O ASN F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 187 removed outlier: 3.873A pdb=" N ASP F 187 " --> pdb=" O GLU F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 215 removed outlier: 3.516A pdb=" N TYR F 215 " --> pdb=" O CYS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 339 No H-bonds generated for 'chain 'F' and resid 337 through 339' Processing helix chain 'F' and resid 364 through 366 No H-bonds generated for 'chain 'F' and resid 364 through 366' Processing helix chain 'F' and resid 397 through 407 removed outlier: 3.571A pdb=" N VAL F 401 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N MET F 402 " --> pdb=" O GLU F 399 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU F 403 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE F 405 " --> pdb=" O MET F 402 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR F 406 " --> pdb=" O GLU F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 417 Processing helix chain 'F' and resid 426 through 437 removed outlier: 3.772A pdb=" N LEU F 434 " --> pdb=" O LYS F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 467 through 476 Processing helix chain 'F' and resid 490 through 493 No H-bonds generated for 'chain 'F' and resid 490 through 493' Processing helix chain 'F' and resid 512 through 515 No H-bonds generated for 'chain 'F' and resid 512 through 515' Processing helix chain 'F' and resid 526 through 528 No H-bonds generated for 'chain 'F' and resid 526 through 528' Processing helix chain 'F' and resid 531 through 541 Processing helix chain 'F' and resid 588 through 593 Processing helix chain 'F' and resid 607 through 621 removed outlier: 3.823A pdb=" N GLU F 610 " --> pdb=" O ASP F 607 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU F 614 " --> pdb=" O LYS F 611 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR F 617 " --> pdb=" O GLU F 614 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET F 621 " --> pdb=" O TYR F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 635 through 645 Processing helix chain 'F' and resid 655 through 671 Processing helix chain 'F' and resid 686 through 702 removed outlier: 3.911A pdb=" N LYS F 701 " --> pdb=" O GLN F 697 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU F 702 " --> pdb=" O ALA F 698 " (cutoff:3.500A) Processing helix chain 'F' and resid 710 through 723 Processing sheet with id= A, first strand: chain '2' and resid 317 through 323 removed outlier: 4.157A pdb=" N GLY 2 322 " --> pdb=" O VAL 2 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE 2 450 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 331 through 334 Processing sheet with id= C, first strand: chain '2' and resid 386 through 391 removed outlier: 3.803A pdb=" N GLN 2 386 " --> pdb=" O LEU 2 410 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 539 through 542 removed outlier: 5.941A pdb=" N ILE 2 679 " --> pdb=" O LEU 2 540 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU 2 542 " --> pdb=" O ILE 2 679 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS 2 681 " --> pdb=" O LEU 2 542 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain '2' and resid 563 through 565 removed outlier: 7.241A pdb=" N VAL 2 603 " --> pdb=" O VAL 2 564 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain '2' and resid 579 through 581 removed outlier: 3.714A pdb=" N GLU 2 592 " --> pdb=" O SER 2 579 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '2' and resid 628 through 631 Processing sheet with id= H, first strand: chain '3' and resid 179 through 185 Processing sheet with id= I, first strand: chain '3' and resid 193 through 196 Processing sheet with id= J, first strand: chain '3' and resid 201 through 203 Processing sheet with id= K, first strand: chain '3' and resid 255 through 259 Processing sheet with id= L, first strand: chain '3' and resid 545 through 549 removed outlier: 3.916A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA 3 515 " --> pdb=" O ILE 3 472 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '3' and resid 494 through 497 removed outlier: 3.775A pdb=" N VAL 3 495 " --> pdb=" O LEU 3 506 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE 3 497 " --> pdb=" O THR 3 504 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '4' and resid 241 through 243 removed outlier: 3.631A pdb=" N LEU 4 243 " --> pdb=" O ARG 4 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '4' and resid 325 through 328 removed outlier: 3.503A pdb=" N GLY 4 437 " --> pdb=" O ILE 4 326 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL 4 435 " --> pdb=" O LEU 4 328 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS 4 465 " --> pdb=" O THR 4 436 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '4' and resid 347 through 349 Processing sheet with id= Q, first strand: chain '4' and resid 414 through 417 removed outlier: 3.798A pdb=" N LYS 4 398 " --> pdb=" O ARG 4 334 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '4' and resid 440 through 442 removed outlier: 3.702A pdb=" N LYS 4 458 " --> pdb=" O ILE 4 442 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '4' and resid 704 through 708 removed outlier: 3.796A pdb=" N ALA 4 675 " --> pdb=" O LEU 4 566 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY 4 568 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '4' and resid 606 through 608 removed outlier: 3.826A pdb=" N GLN 4 613 " --> pdb=" O ASP 4 608 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '4' and resid 654 through 656 removed outlier: 4.346A pdb=" N ILE 4 656 " --> pdb=" O THR 4 663 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR 4 663 " --> pdb=" O ILE 4 656 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '5' and resid 61 through 64 Processing sheet with id= W, first strand: chain '5' and resid 159 through 161 Processing sheet with id= X, first strand: chain '5' and resid 180 through 183 removed outlier: 4.774A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '5' and resid 257 through 259 removed outlier: 3.817A pdb=" N LEU 5 258 " --> pdb=" O LEU 5 274 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '5' and resid 412 through 416 removed outlier: 6.892A pdb=" N MET 5 552 " --> pdb=" O LEU 5 413 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU 5 415 " --> pdb=" O MET 5 552 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE 5 554 " --> pdb=" O LEU 5 415 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain '5' and resid 436 through 439 removed outlier: 7.013A pdb=" N VAL 5 476 " --> pdb=" O VAL 5 437 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N THR 5 439 " --> pdb=" O VAL 5 476 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N CYS 5 478 " --> pdb=" O THR 5 439 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N SER 5 518 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE 5 479 " --> pdb=" O SER 5 518 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU 5 520 " --> pdb=" O ILE 5 479 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain '5' and resid 175 through 178 removed outlier: 6.969A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain '5' and resid 452 through 456 removed outlier: 3.573A pdb=" N SER 5 452 " --> pdb=" O GLY 5 466 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY 5 466 " --> pdb=" O SER 5 452 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN 5 454 " --> pdb=" O LEU 5 464 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU 5 464 " --> pdb=" O GLN 5 454 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP 5 456 " --> pdb=" O PHE 5 462 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE 5 462 " --> pdb=" O ASP 5 456 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain '6' and resid 151 through 154 removed outlier: 3.817A pdb=" N SER 6 266 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 6 153 " --> pdb=" O SER 6 266 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE 6 268 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain '6' and resid 291 through 293 removed outlier: 3.742A pdb=" N GLY 6 292 " --> pdb=" O CYS 6 395 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS 6 395 " --> pdb=" O GLY 6 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain '6' and resid 301 through 303 removed outlier: 3.523A pdb=" N ARG 6 301 " --> pdb=" O TRP 6 356 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU 6 354 " --> pdb=" O GLU 6 303 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain '6' and resid 360 through 362 Processing sheet with id= AH, first strand: chain '6' and resid 403 through 406 removed outlier: 4.184A pdb=" N THR 6 449 " --> pdb=" O ASP 6 406 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain '6' and resid 572 through 574 removed outlier: 7.211A pdb=" N VAL 6 573 " --> pdb=" O ILE 6 678 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ALA 6 680 " --> pdb=" O VAL 6 573 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU 6 679 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL 6 596 " --> pdb=" O ILE 6 635 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain '6' and resid 660 through 664 Processing sheet with id= AK, first strand: chain '7' and resid 79 through 81 removed outlier: 6.680A pdb=" N TYR 7 203 " --> pdb=" O ILE 7 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain '7' and resid 238 through 240 Processing sheet with id= AM, first strand: chain '7' and resid 244 through 246 Processing sheet with id= AN, first strand: chain '7' and resid 259 through 261 removed outlier: 4.631A pdb=" N ALA 7 259 " --> pdb=" O SER 7 301 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE 7 299 " --> pdb=" O THR 7 261 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '7' and resid 480 through 483 removed outlier: 6.724A pdb=" N ILE 7 520 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N THR 7 483 " --> pdb=" O ILE 7 520 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N CYS 7 522 " --> pdb=" O THR 7 483 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain '7' and resid 496 through 498 removed outlier: 3.695A pdb=" N MET 7 498 " --> pdb=" O ILE 7 507 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE 7 507 " --> pdb=" O MET 7 498 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '7' and resid 254 through 257 removed outlier: 6.817A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'A' and resid 317 through 323 removed outlier: 4.157A pdb=" N GLY A 322 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 450 " --> pdb=" O LYS A 431 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'A' and resid 331 through 334 Processing sheet with id= AT, first strand: chain 'A' and resid 386 through 391 removed outlier: 3.802A pdb=" N GLN A 386 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'A' and resid 539 through 542 removed outlier: 5.941A pdb=" N ILE A 679 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU A 542 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N CYS A 681 " --> pdb=" O LEU A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'A' and resid 563 through 565 removed outlier: 7.242A pdb=" N VAL A 603 " --> pdb=" O VAL A 564 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'A' and resid 579 through 581 removed outlier: 3.714A pdb=" N GLU A 592 " --> pdb=" O SER A 579 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'A' and resid 628 through 631 Processing sheet with id= AY, first strand: chain 'B' and resid 179 through 185 Processing sheet with id= AZ, first strand: chain 'B' and resid 193 through 196 Processing sheet with id= BA, first strand: chain 'B' and resid 201 through 203 Processing sheet with id= BB, first strand: chain 'B' and resid 255 through 259 Processing sheet with id= BC, first strand: chain 'B' and resid 545 through 549 removed outlier: 3.918A pdb=" N GLY B 409 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 515 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'B' and resid 494 through 497 removed outlier: 3.775A pdb=" N VAL B 495 " --> pdb=" O LEU B 506 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 497 " --> pdb=" O THR B 504 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'C' and resid 241 through 243 removed outlier: 3.630A pdb=" N LEU C 243 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.504A pdb=" N GLY C 437 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 435 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS C 465 " --> pdb=" O THR C 436 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'C' and resid 347 through 349 Processing sheet with id= BH, first strand: chain 'C' and resid 414 through 417 removed outlier: 3.798A pdb=" N LYS C 398 " --> pdb=" O ARG C 334 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG C 334 " --> pdb=" O LYS C 398 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLN C 400 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL C 332 " --> pdb=" O GLN C 400 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'C' and resid 440 through 442 removed outlier: 3.703A pdb=" N LYS C 458 " --> pdb=" O ILE C 442 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'C' and resid 704 through 708 removed outlier: 3.796A pdb=" N ALA C 675 " --> pdb=" O LEU C 566 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY C 568 " --> pdb=" O ALA C 675 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'C' and resid 606 through 608 removed outlier: 3.826A pdb=" N GLN C 613 " --> pdb=" O ASP C 608 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'C' and resid 654 through 656 removed outlier: 4.346A pdb=" N ILE C 656 " --> pdb=" O THR C 663 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 663 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'D' and resid 61 through 64 Processing sheet with id= BN, first strand: chain 'D' and resid 159 through 161 Processing sheet with id= BO, first strand: chain 'D' and resid 180 through 183 removed outlier: 4.775A pdb=" N SER D 180 " --> pdb=" O ILE D 244 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'D' and resid 257 through 259 removed outlier: 3.817A pdb=" N LEU D 258 " --> pdb=" O LEU D 274 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'D' and resid 412 through 416 removed outlier: 6.892A pdb=" N MET D 552 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU D 415 " --> pdb=" O MET D 552 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE D 554 " --> pdb=" O LEU D 415 " (cutoff:3.500A) No H-bonds generated for sheet with id= BQ Processing sheet with id= BR, first strand: chain 'D' and resid 436 through 439 removed outlier: 7.014A pdb=" N VAL D 476 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N THR D 439 " --> pdb=" O VAL D 476 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N CYS D 478 " --> pdb=" O THR D 439 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N SER D 518 " --> pdb=" O VAL D 477 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE D 479 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU D 520 " --> pdb=" O ILE D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id= BR Processing sheet with id= BS, first strand: chain 'D' and resid 175 through 178 removed outlier: 6.968A pdb=" N LYS D 249 " --> pdb=" O THR D 177 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'D' and resid 452 through 456 removed outlier: 3.572A pdb=" N SER D 452 " --> pdb=" O GLY D 466 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY D 466 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLN D 454 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU D 464 " --> pdb=" O GLN D 454 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP D 456 " --> pdb=" O PHE D 462 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE D 462 " --> pdb=" O ASP D 456 " (cutoff:3.500A) No H-bonds generated for sheet with id= BT Processing sheet with id= BU, first strand: chain 'E' and resid 151 through 154 removed outlier: 3.817A pdb=" N SER E 266 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE E 153 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE E 268 " --> pdb=" O ILE E 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= BU Processing sheet with id= BV, first strand: chain 'E' and resid 291 through 293 removed outlier: 3.742A pdb=" N GLY E 292 " --> pdb=" O CYS E 395 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS E 395 " --> pdb=" O GLY E 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'E' and resid 301 through 303 removed outlier: 3.524A pdb=" N ARG E 301 " --> pdb=" O TRP E 356 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 354 " --> pdb=" O GLU E 303 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'E' and resid 360 through 362 Processing sheet with id= BY, first strand: chain 'E' and resid 403 through 406 removed outlier: 4.184A pdb=" N THR E 449 " --> pdb=" O ASP E 406 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'E' and resid 572 through 574 removed outlier: 7.211A pdb=" N VAL E 573 " --> pdb=" O ILE E 678 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ALA E 680 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 679 " --> pdb=" O CYS E 636 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL E 596 " --> pdb=" O ILE E 635 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'E' and resid 660 through 664 Processing sheet with id= CB, first strand: chain 'F' and resid 79 through 81 removed outlier: 6.680A pdb=" N TYR F 203 " --> pdb=" O ILE F 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= CB Processing sheet with id= CC, first strand: chain 'F' and resid 238 through 240 Processing sheet with id= CD, first strand: chain 'F' and resid 244 through 246 Processing sheet with id= CE, first strand: chain 'F' and resid 259 through 261 removed outlier: 4.631A pdb=" N ALA F 259 " --> pdb=" O SER F 301 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE F 299 " --> pdb=" O THR F 261 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'F' and resid 480 through 483 removed outlier: 6.724A pdb=" N ILE F 520 " --> pdb=" O VAL F 481 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N THR F 483 " --> pdb=" O ILE F 520 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS F 522 " --> pdb=" O THR F 483 " (cutoff:3.500A) No H-bonds generated for sheet with id= CF Processing sheet with id= CG, first strand: chain 'F' and resid 496 through 498 removed outlier: 3.696A pdb=" N MET F 498 " --> pdb=" O ILE F 507 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE F 507 " --> pdb=" O MET F 498 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'F' and resid 254 through 257 removed outlier: 6.817A pdb=" N LYS F 306 " --> pdb=" O GLU F 256 " (cutoff:3.500A) 1662 hydrogen bonds defined for protein. 4470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 143 hydrogen bonds 286 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 113 stacking parallelities Total time for adding SS restraints: 20.00 Time building geometry restraints manager: 19.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 20414 1.34 - 1.47: 15127 1.47 - 1.61: 27705 1.61 - 1.74: 28 1.74 - 1.87: 440 Bond restraints: 63714 Sorted by residual: bond pdb=" CA ILE 5 87 " pdb=" CB ILE 5 87 " ideal model delta sigma weight residual 1.539 1.517 0.022 5.40e-03 3.43e+04 1.67e+01 bond pdb=" CA ILE D 87 " pdb=" CB ILE D 87 " ideal model delta sigma weight residual 1.539 1.517 0.022 5.40e-03 3.43e+04 1.59e+01 bond pdb=" C LEU F 343 " pdb=" N SER F 344 " ideal model delta sigma weight residual 1.331 1.251 0.080 2.83e-02 1.25e+03 8.00e+00 bond pdb=" C LEU 7 343 " pdb=" N SER 7 344 " ideal model delta sigma weight residual 1.331 1.251 0.080 2.83e-02 1.25e+03 7.96e+00 bond pdb=" C VAL E 415 " pdb=" N LYS E 416 " ideal model delta sigma weight residual 1.331 1.273 0.058 2.07e-02 2.33e+03 7.72e+00 ... (remaining 63709 not shown) Histogram of bond angle deviations from ideal: 97.62 - 107.18: 2989 107.18 - 116.74: 42464 116.74 - 126.31: 40174 126.31 - 135.87: 1065 135.87 - 145.44: 20 Bond angle restraints: 86712 Sorted by residual: angle pdb=" N GLY 6 399 " pdb=" CA GLY 6 399 " pdb=" C GLY 6 399 " ideal model delta sigma weight residual 114.67 131.75 -17.08 1.10e+00 8.26e-01 2.41e+02 angle pdb=" N GLY E 399 " pdb=" CA GLY E 399 " pdb=" C GLY E 399 " ideal model delta sigma weight residual 114.67 131.74 -17.07 1.10e+00 8.26e-01 2.41e+02 angle pdb=" N HIS 7 620 " pdb=" CA HIS 7 620 " pdb=" C HIS 7 620 " ideal model delta sigma weight residual 114.75 100.09 14.66 1.26e+00 6.30e-01 1.35e+02 angle pdb=" N HIS F 620 " pdb=" CA HIS F 620 " pdb=" C HIS F 620 " ideal model delta sigma weight residual 114.75 100.13 14.62 1.26e+00 6.30e-01 1.35e+02 angle pdb=" C GLU 5 269 " pdb=" N MET 5 270 " pdb=" CA MET 5 270 " ideal model delta sigma weight residual 122.31 143.19 -20.88 2.34e+00 1.83e-01 7.96e+01 ... (remaining 86707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.09: 36860 26.09 - 52.18: 1778 52.18 - 78.28: 245 78.28 - 104.37: 14 104.37 - 130.46: 3 Dihedral angle restraints: 38900 sinusoidal: 16558 harmonic: 22342 Sorted by residual: dihedral pdb=" CA ILE C 360 " pdb=" C ILE C 360 " pdb=" N ASP C 361 " pdb=" CA ASP C 361 " ideal model delta harmonic sigma weight residual 180.00 -125.34 -54.66 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA ILE 4 360 " pdb=" C ILE 4 360 " pdb=" N ASP 4 361 " pdb=" CA ASP 4 361 " ideal model delta harmonic sigma weight residual -180.00 -125.36 -54.64 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA PRO F 501 " pdb=" C PRO F 501 " pdb=" N VAL F 502 " pdb=" CA VAL F 502 " ideal model delta harmonic sigma weight residual -180.00 -127.04 -52.96 0 5.00e+00 4.00e-02 1.12e+02 ... (remaining 38897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 8054 0.077 - 0.154: 1827 0.154 - 0.230: 180 0.230 - 0.307: 17 0.307 - 0.384: 4 Chirality restraints: 10082 Sorted by residual: chirality pdb=" CG LEU A 306 " pdb=" CB LEU A 306 " pdb=" CD1 LEU A 306 " pdb=" CD2 LEU A 306 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CG LEU 2 306 " pdb=" CB LEU 2 306 " pdb=" CD1 LEU 2 306 " pdb=" CD2 LEU 2 306 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE 2 636 " pdb=" CA ILE 2 636 " pdb=" CG1 ILE 2 636 " pdb=" CG2 ILE 2 636 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 10079 not shown) Planarity restraints: 10746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 3 211 " 0.035 2.00e-02 2.50e+03 2.53e-02 1.28e+01 pdb=" CG TYR 3 211 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR 3 211 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR 3 211 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR 3 211 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR 3 211 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR 3 211 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR 3 211 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 211 " 0.034 2.00e-02 2.50e+03 2.52e-02 1.27e+01 pdb=" CG TYR B 211 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR B 211 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 211 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 211 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 211 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 211 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 211 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 461 " -0.056 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO F 462 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO F 462 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO F 462 " -0.043 5.00e-02 4.00e+02 ... (remaining 10743 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 11504 2.77 - 3.30: 56896 3.30 - 3.83: 96219 3.83 - 4.37: 104960 4.37 - 4.90: 176648 Nonbonded interactions: 446227 Sorted by model distance: nonbonded pdb=" OH TYR F 482 " pdb=" OD2 ASP F 524 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR 7 482 " pdb=" OD2 ASP 7 524 " model vdw 2.234 2.440 nonbonded pdb=" O HIS 3 564 " pdb=" OG1 THR 3 568 " model vdw 2.243 2.440 nonbonded pdb=" O HIS B 564 " pdb=" OG1 THR B 568 " model vdw 2.244 2.440 nonbonded pdb=" O VAL F 616 " pdb=" O VAL F 619 " model vdw 2.245 3.040 ... (remaining 446222 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 '2' selection = chain 'A' } ncs_group { reference = chain '3' selection = chain 'B' } ncs_group { reference = chain '4' selection = chain 'C' } ncs_group { reference = chain '5' selection = chain 'D' } ncs_group { reference = chain '6' selection = chain 'E' } ncs_group { reference = chain '7' selection = chain 'F' } 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 5.940 Check model and map are aligned: 0.680 Set scattering table: 0.440 Process input model: 129.990 Find NCS groups from input model: 4.760 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 63714 Z= 0.542 Angle : 1.239 20.878 86712 Z= 0.671 Chirality : 0.063 0.384 10082 Planarity : 0.007 0.085 10746 Dihedral : 14.591 130.462 24350 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.22 % Favored : 87.63 % Rotamer: Outliers : 1.24 % Allowed : 5.08 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 2.30 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -4.81 (0.07), residues: 7548 helix: -3.23 (0.07), residues: 2542 sheet: -2.71 (0.15), residues: 1018 loop : -3.35 (0.08), residues: 3988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 181 HIS 0.020 0.003 HIS 4 723 PHE 0.041 0.004 PHE D 31 TYR 0.062 0.003 TYR 3 211 ARG 0.016 0.001 ARG 6 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1750 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1666 time to evaluate : 5.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 294, in __init__ self.caller(self.optimize_sidechains) 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 600, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 180, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 131, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 99, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 209, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 196, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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