Starting phenix.real_space_refine on Wed Mar 20 17:53:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tm0_25992/03_2024/7tm0_25992.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tm0_25992/03_2024/7tm0_25992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tm0_25992/03_2024/7tm0_25992.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tm0_25992/03_2024/7tm0_25992.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tm0_25992/03_2024/7tm0_25992.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tm0_25992/03_2024/7tm0_25992.pdb" } resolution = 3.1 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= 0.051 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: 4 Type Number sf(0) Gaussians S 134 5.16 5 C 17448 2.51 5 N 4990 2.21 5 O 5391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27963 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 7054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7054 Classifications: {'peptide': 1016} Incomplete info: {'truncation_to_alanine': 287} Link IDs: {'PTRANS': 56, 'TRANS': 959} Chain breaks: 10 Unresolved non-hydrogen bonds: 979 Unresolved non-hydrogen angles: 1259 Unresolved non-hydrogen dihedrals: 797 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 16, 'ASN:plan1': 20, 'TRP:plan': 2, 'ASP:plan': 27, 'PHE:plan': 13, 'GLU:plan': 22, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 600 Chain: "B" Number of atoms: 6746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 6746 Classifications: {'peptide': 1015} Incomplete info: {'truncation_to_alanine': 374} Link IDs: {'PTRANS': 56, 'TRANS': 958} Chain breaks: 10 Unresolved non-hydrogen bonds: 1297 Unresolved non-hydrogen angles: 1669 Unresolved non-hydrogen dihedrals: 1061 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 27, 'TYR:plan': 17, 'ASN:plan1': 31, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 26, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 745 Chain: "C" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 6652 Classifications: {'peptide': 1012} Incomplete info: {'truncation_to_alanine': 391} Link IDs: {'PTRANS': 56, 'TRANS': 955} Chain breaks: 12 Unresolved non-hydrogen bonds: 1370 Unresolved non-hydrogen angles: 1760 Unresolved non-hydrogen dihedrals: 1121 Unresolved non-hydrogen chiralities: 136 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 21, 'TYR:plan': 18, 'ASN:plan1': 26, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 27, 'GLU:plan': 25, 'ASP:plan': 29} Unresolved non-hydrogen planarities: 787 Chain: "D" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 528 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 171 Chain: "E" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 592 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 11, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 234 Chain: "F" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 528 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 171 Chain: "G" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 592 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 11, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 234 Chain: "H" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 528 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 171 Chain: "I" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 592 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 11, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 234 Chain: "J" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 624 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 377 Unresolved non-hydrogen angles: 494 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 235 Chain: "K" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 508 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 152 Chain: "L" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 630 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 495 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 235 Chain: "M" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 508 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 152 Chain: "N" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 630 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 495 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 235 Chain: "O" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 523 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 152 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 16.06, per 1000 atoms: 0.57 Number of scatterers: 27963 At special positions: 0 Unit cell: (152.583, 155.112, 197.262, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 134 16.00 O 5391 8.00 N 4990 7.00 C 17448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.10 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.07 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 707 " - pdb=" SG CYS C 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.09 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.13 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS B 707 " distance=2.10 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.10 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.12 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.14 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.16 Simple disulfide: pdb=" SG CYS B 883 " - pdb=" SG CYS C 707 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.10 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.19 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.05 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 89 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 89 " 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 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A9301 " - " ASN A 343 " " NAG A9302 " - " ASN A 165 " " NAG A9303 " - " ASN A 282 " " NAG A9304 " - " ASN A 17 " " NAG A9305 " - " ASN A 234 " " NAG A9306 " - " ASN A 61 " " NAG A9307 " - " ASN A 122 " " NAG A9308 " - " ASN A 603 " " NAG A9309 " - " ASN A 657 " " NAG A9310 " - " ASN A 709 " " NAG A9311 " - " ASN A 717 " " NAG A9312 " - " ASN A 801 " " NAG A9313 " - " ASN A1074 " " NAG A9314 " - " ASN A1134 " " NAG A9315 " - " ASN A1098 " " NAG A9316 " - " ASN A 331 " " NAG A9317 " - " ASN A 616 " " NAG B9301 " - " ASN B 343 " " NAG B9302 " - " ASN B 165 " " NAG B9303 " - " ASN B 282 " " NAG B9304 " - " ASN B 17 " " NAG B9305 " - " ASN B 234 " " NAG B9306 " - " ASN B 61 " " NAG B9307 " - " ASN B 122 " " NAG B9308 " - " ASN B 603 " " NAG B9309 " - " ASN B 657 " " NAG B9310 " - " ASN B 709 " " NAG B9311 " - " ASN B 717 " " NAG B9312 " - " ASN B1074 " " NAG B9313 " - " ASN B1134 " " NAG B9314 " - " ASN B 616 " " NAG B9315 " - " ASN B1098 " " NAG B9316 " - " ASN B 331 " " NAG C9301 " - " ASN C 343 " " NAG C9302 " - " ASN C 165 " " NAG C9303 " - " ASN C 282 " " NAG C9304 " - " ASN C 17 " " NAG C9305 " - " ASN C 234 " " NAG C9306 " - " ASN C 61 " " NAG C9307 " - " ASN C 122 " " NAG C9308 " - " ASN C 616 " " NAG C9309 " - " ASN C 657 " " NAG C9310 " - " ASN C 709 " " NAG C9311 " - " ASN C 801 " " NAG C9312 " - " ASN C1074 " " NAG C9313 " - " ASN C1134 " " NAG C9314 " - " ASN C 603 " " NAG C9315 " - " ASN C 717 " " NAG C9316 " - " ASN C1098 " " NAG C9317 " - " ASN C 331 " " NAG P 1 " - " ASN B 801 " Time building additional restraints: 11.20 Conformation dependent library (CDL) restraints added in 5.8 seconds 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8158 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 85 sheets defined 19.8% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.24 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.746A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.432A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 removed outlier: 4.078A pdb=" N GLY A 757 " --> pdb=" O LEU A 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.796A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 851 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.723A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.720A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.148A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.593A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.973A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.747A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.433A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.558A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.811A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 851 through 855 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.786A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.995A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.734A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.628A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.569A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.746A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.432A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.766A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.575A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.868A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.070A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.758A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.580A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.580A pdb=" N TYR L 32 " --> pdb=" O PHE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 65 Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'M' and resid 30 through 32 No H-bonds generated for 'chain 'M' and resid 30 through 32' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.580A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'O' and resid 30 through 32 No H-bonds generated for 'chain 'O' and resid 30 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.185A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.756A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.066A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.167A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 13.074A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.018A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.576A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.240A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.245A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.667A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.503A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.635A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.357A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.440A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.440A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.395A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB8, first strand: chain 'A' and resid 796 through 797 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.894A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.184A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.887A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS C 537 " --> pdb=" O LEU C 552 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.068A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.167A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 13.074A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 13.017A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 11.224A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.575A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.277A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.666A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.503A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.961A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.508A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.508A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.371A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AD7, first strand: chain 'B' and resid 796 through 797 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.828A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.182A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.068A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.167A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 13.075A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 13.017A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N CYS C 136 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TYR C 160 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP C 138 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ARG C 158 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.575A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.268A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.667A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.503A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.639A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.443A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.443A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.484A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 796 through 797 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.841A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 4 through 7 removed outlier: 4.095A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 67 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.652A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU D 33 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.652A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU D 33 " --> pdb=" O SER D 49 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.643A pdb=" N MET E 34 " --> pdb=" O PHE E 50 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AG2, first strand: chain 'F' and resid 4 through 7 removed outlier: 4.095A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.651A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.651A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AG6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.644A pdb=" N MET G 34 " --> pdb=" O PHE G 50 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AG8, first strand: chain 'H' and resid 4 through 7 removed outlier: 4.095A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.651A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU H 33 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.651A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU H 33 " --> pdb=" O SER H 49 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AH3, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.645A pdb=" N MET I 34 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AH5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AH6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.858A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.735A pdb=" N ASN J 116 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AH9, first strand: chain 'K' and resid 10 through 11 removed outlier: 7.002A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 10 through 11 Processing sheet with id=AI2, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AI3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.856A pdb=" N ILE L 34 " --> pdb=" O TRP L 50 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TRP L 50 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP L 36 " --> pdb=" O MET L 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.735A pdb=" N ASN L 116 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AI6, first strand: chain 'M' and resid 10 through 11 removed outlier: 7.002A pdb=" N LEU M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR M 50 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'M' and resid 10 through 11 Processing sheet with id=AI8, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AI9, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.857A pdb=" N ILE N 34 " --> pdb=" O TRP N 50 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TRP N 50 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP N 36 " --> pdb=" O MET N 48 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.735A pdb=" N ASN N 116 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AJ3, first strand: chain 'O' and resid 10 through 12 removed outlier: 5.871A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR O 50 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'O' and resid 10 through 12 removed outlier: 5.871A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) 1610 hydrogen bonds defined for protein. 4098 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: 19.01 Time building geometry restraints manager: 11.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5425 1.32 - 1.45: 6734 1.45 - 1.58: 16083 1.58 - 1.71: 0 1.71 - 1.84: 158 Bond restraints: 28400 Sorted by residual: bond pdb=" C ASN B 616 " pdb=" O ASN B 616 " ideal model delta sigma weight residual 1.234 1.320 -0.086 1.22e-02 6.72e+03 4.93e+01 bond pdb=" C CYS C 617 " pdb=" O CYS C 617 " ideal model delta sigma weight residual 1.237 1.311 -0.074 1.17e-02 7.31e+03 3.99e+01 bond pdb=" C CYS C 738 " pdb=" O CYS C 738 " ideal model delta sigma weight residual 1.236 1.312 -0.076 1.29e-02 6.01e+03 3.46e+01 bond pdb=" C ASN B 616 " pdb=" N CYS B 617 " ideal model delta sigma weight residual 1.335 1.263 0.072 1.35e-02 5.49e+03 2.87e+01 bond pdb=" CA CYS C 617 " pdb=" C CYS C 617 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.30e-02 5.92e+03 2.62e+01 ... (remaining 28395 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.06: 1025 107.06 - 113.86: 15664 113.86 - 120.66: 11028 120.66 - 127.47: 11285 127.47 - 134.27: 65 Bond angle restraints: 39067 Sorted by residual: angle pdb=" C LEU B 861 " pdb=" N PRO B 862 " pdb=" CA PRO B 862 " ideal model delta sigma weight residual 119.66 126.16 -6.50 7.20e-01 1.93e+00 8.16e+01 angle pdb=" C LEU C 861 " pdb=" N PRO C 862 " pdb=" CA PRO C 862 " ideal model delta sigma weight residual 119.66 126.13 -6.47 7.20e-01 1.93e+00 8.07e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 126.03 -6.37 7.20e-01 1.93e+00 7.83e+01 angle pdb=" C THR A 791 " pdb=" N PRO A 792 " pdb=" CA PRO A 792 " ideal model delta sigma weight residual 119.66 126.00 -6.34 7.20e-01 1.93e+00 7.75e+01 angle pdb=" N PHE C 306 " pdb=" CA PHE C 306 " pdb=" C PHE C 306 " ideal model delta sigma weight residual 113.20 102.66 10.54 1.21e+00 6.83e-01 7.59e+01 ... (remaining 39062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 17065 17.89 - 35.78: 364 35.78 - 53.67: 88 53.67 - 71.55: 19 71.55 - 89.44: 7 Dihedral angle restraints: 17543 sinusoidal: 4952 harmonic: 12591 Sorted by residual: dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 96 " pdb=" CB CYS I 96 " ideal model delta sinusoidal sigma weight residual 93.00 53.27 39.73 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 53.28 39.72 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 96 " pdb=" CB CYS G 96 " ideal model delta sinusoidal sigma weight residual 93.00 53.28 39.72 1 1.00e+01 1.00e-02 2.22e+01 ... (remaining 17540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.273: 4856 0.273 - 0.545: 49 0.545 - 0.818: 0 0.818 - 1.091: 0 1.091 - 1.363: 1 Chirality restraints: 4906 Sorted by residual: chirality pdb=" C1 NAG B9315 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B9315 " pdb=" O5 NAG B9315 " both_signs ideal model delta sigma weight residual False -2.40 -1.04 -1.36 2.00e-01 2.50e+01 4.65e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.37e+01 chirality pdb=" CA ASN C 978 " pdb=" N ASN C 978 " pdb=" C ASN C 978 " pdb=" CB ASN C 978 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 4903 not shown) Planarity restraints: 5323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " -0.101 2.00e-02 2.50e+03 1.64e-01 3.35e+02 pdb=" CG ASN A1134 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " -0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " 0.290 2.00e-02 2.50e+03 pdb=" C1 NAG A9314 " -0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.092 2.00e-02 2.50e+03 1.12e-01 1.57e+02 pdb=" CG ASN B 331 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.190 2.00e-02 2.50e+03 pdb=" C1 NAG B9316 " -0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1098 " 0.060 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" CG ASN B1098 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B1098 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN B1098 " -0.181 2.00e-02 2.50e+03 pdb=" C1 NAG B9315 " 0.111 2.00e-02 2.50e+03 ... (remaining 5320 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6742 2.79 - 3.32: 22788 3.32 - 3.85: 41409 3.85 - 4.37: 45254 4.37 - 4.90: 79526 Nonbonded interactions: 195719 Sorted by model distance: nonbonded pdb=" N PHE C 306 " pdb=" N THR C 307 " model vdw 2.264 2.560 nonbonded pdb=" OD1 ASP C 979 " pdb=" N ILE C 980 " model vdw 2.382 2.520 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.418 2.440 nonbonded pdb=" O GLY A 889 " pdb=" NZ LYS B1045 " model vdw 2.442 2.520 nonbonded pdb=" O TYR A 473 " pdb=" C GLN A 474 " model vdw 2.447 3.270 ... (remaining 195714 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 14 through 18 or resid 23 through 31 or (resid 32 through \ 34 and (name N or name CA or name C or name O or name CB )) or resid 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 50 or (resid 51 through 53 and (name N or name CA or name C or name O or name \ CB )) or resid 54 through 55 or (resid 56 and (name N or name CA or name C or na \ me O or name CB )) or resid 57 through 59 or (resid 60 and (name N or name CA or \ name C or name O or name CB )) or resid 61 or (resid 62 through 63 and (name N \ or name CA or name C or name O or name CB )) or resid 64 through 65 or (resid 66 \ through 81 and (name N or name CA or name C or name O or name CB )) or resid 82 \ or (resid 83 through 84 and (name N or name CA or name C or name O or name CB ) \ ) or resid 85 or (resid 86 through 88 and (name N or name CA or name C or name O \ or name CB )) or resid 89 through 94 or (resid 95 through 102 and (name N or na \ me CA or name C or name O or name CB )) or resid 103 or (resid 104 through 106 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 107 through 11 \ 3 and (name N or name CA or name C or name O or name CB )) or (resid 116 through \ 121 and (name N or name CA or name C or name O or name CB )) or resid 122 throu \ gh 128 or (resid 129 through 130 and (name N or name CA or name C or name O or n \ ame CB )) or resid 131 through 132 or (resid 133 through 135 and (name N or name \ CA or name C or name O or name CB )) or resid 136 through 139 or (resid 140 thr \ ough 164 and (name N or name CA or name C or name O or name CB )) or resid 165 t \ hrough 167 or (resid 168 through 173 and (name N or name CA or name C or name O \ or name CB )) or resid 174 through 186 or (resid 187 through 191 and (name N or \ name CA or name C or name O or name CB )) or resid 192 through 194 or (resid 195 \ through 196 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 99 through 201 or (resid 202 and (name N or name CA or name C or name O or name \ CB )) or resid 203 through 205 or (resid 206 through 208 and (name N or name CA \ or name C or name O or name CB )) or resid 209 through 215 or (resid 216 and (na \ me N or name CA or name C or name O or name CB )) or resid 217 through 219 or (r \ esid 220 through 224 and (name N or name CA or name C or name O or name CB )) or \ resid 225 or (resid 226 through 229 and (name N or name CA or name C or name O \ or name CB )) or resid 230 or (resid 231 and (name N or name CA or name C or nam \ e O or name CB )) or resid 232 through 234 or (resid 235 through 245 and (name N \ or name CA or name C or name O or name CB )) or resid 262 through 266 or (resid \ 267 and (name N or name CA or name C or name O or name CB )) or resid 268 throu \ gh 270 or (resid 271 and (name N or name CA or name C or name O or name CB )) or \ resid 272 or (resid 273 and (name N or name CA or name C or name O or name CB ) \ ) or resid 274 through 277 or (resid 278 and (name N or name CA or name C or nam \ e O or name CB )) or resid 279 through 303 or (resid 304 through 305 and (name N \ or name CA or name C or name O or name CB )) or resid 306 or (resid 307 through \ 309 and (name N or name CA or name C or name O or name CB )) or resid 310 throu \ gh 316 or (resid 317 and (name N or name CA or name C or name O or name CB )) or \ resid 318 or (resid 319 through 321 and (name N or name CA or name C or name O \ or name CB )) or resid 322 or (resid 323 through 329 and (name N or name CA or n \ ame C or name O or name CB )) or resid 330 through 334 or (resid 335 and (name N \ or name CA or name C or name O or name CB )) or resid 336 through 346 or (resid \ 347 through 360 and (name N or name CA or name C or name O or name CB )) or res \ id 361 or (resid 362 through 378 and (name N or name CA or name C or name O or n \ ame CB )) or resid 379 through 385 or (resid 386 through 390 and (name N or name \ CA or name C or name O or name CB )) or resid 391 or (resid 392 through 403 and \ (name N or name CA or name C or name O or name CB )) or resid 404 through 424 o \ r (resid 425 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 26 through 428 or (resid 429 through 430 and (name N or name CA or name C or nam \ e O or name CB )) or resid 431 through 514 or (resid 515 through 520 and (name N \ or name CA or name C or name O or name CB )) or resid 521 through 523 or (resid \ 524 and (name N or name CA or name C or name O or name CB )) or resid 525 throu \ gh 527 or (resid 528 through 537 and (name N or name CA or name C or name O or n \ ame CB )) or resid 538 or (resid 539 through 544 and (name N or name CA or name \ C or name O or name CB )) or resid 545 or (resid 546 through 547 and (name N or \ name CA or name C or name O or name CB )) or resid 548 or (resid 549 and (name N \ or name CA or name C or name O or name CB )) or resid 550 or (resid 551 through \ 558 and (name N or name CA or name C or name O or name CB )) or resid 559 throu \ gh 571 or (resid 572 through 576 and (name N or name CA or name C or name O or n \ ame CB )) or resid 577 or (resid 578 and (name N or name CA or name C or name O \ or name CB )) or resid 579 or (resid 580 through 588 and (name N or name CA or n \ ame C or name O or name CB )) or resid 589 through 591 or (resid 592 and (name N \ or name CA or name C or name O or name CB )) or resid 593 through 604 or (resid \ 605 and (name N or name CA or name C or name O or name CB )) or resid 606 throu \ gh 614 or (resid 615 and (name N or name CA or name C or name O or name CB )) or \ resid 616 through 617 or (resid 618 through 620 and (name N or name CA or name \ C or name O or name CB )) or resid 621 through 644 or (resid 645 and (name N or \ name CA or name C or name O or name CB )) or resid 646 through 660 or (resid 661 \ and (name N or name CA or name C or name O or name CB )) or resid 662 through 6 \ 89 or (resid 690 through 691 and (name N or name CA or name C or name O or name \ CB )) or resid 692 through 701 or (resid 702 and (name N or name CA or name C or \ name O or name CB )) or resid 703 or (resid 704 and (name N or name CA or name \ C or name O or name CB )) or resid 705 through 720 or (resid 721 and (name N or \ name CA or name C or name O or name CB )) or resid 722 through 734 or (resid 735 \ and (name N or name CA or name C or name O or name CB )) or resid 736 through 7 \ 45 or (resid 746 through 748 and (name N or name CA or name C or name O or name \ CB )) or resid 749 or (resid 750 through 751 and (name N or name CA or name C or \ name O or name CB )) or resid 752 through 758 or (resid 759 and (name N or name \ CA or name C or name O or name CB )) or resid 760 through 784 or (resid 785 thr \ ough 786 and (name N or name CA or name C or name O or name CB )) or resid 787 t \ hrough 810 or (resid 811 and (name N or name CA or name C or name O or name CB ) \ ) or resid 812 through 850 or (resid 851 through 852 and (name N or name CA or n \ ame C or name O or name CB )) or resid 853 or (resid 854 through 855 and (name N \ or name CA or name C or name O or name CB )) or resid 856 through 985 or (resid \ 986 and (name N or name CA or name C or name O or name CB )) or resid 987 throu \ gh 990 or (resid 991 and (name N or name CA or name C or name O or name CB )) or \ resid 992 through 994 or (resid 995 and (name N or name CA or name C or name O \ or name CB )) or resid 996 through 1083 or (resid 1084 and (name N or name CA or \ name C or name O or name CB )) or resid 1085 through 1099 or (resid 1100 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1101 through 1126 or \ (resid 1127 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 128 through 1141 or (resid 1142 and (name N or name CA or name C or name O or na \ me CB )) or resid 1143 through 1145 or resid 9301 through 9316)) selection = (chain 'B' and (resid 14 through 30 or (resid 31 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 or (resid 36 and (name N or nam \ e CA or name C or name O or name CB )) or resid 37 through 46 or (resid 47 and ( \ name N or name CA or name C or name O or name CB )) or resid 48 through 51 or (r \ esid 52 through 53 and (name N or name CA or name C or name O or name CB )) or r \ esid 54 through 55 or (resid 56 and (name N or name CA or name C or name O or na \ me CB )) or resid 57 through 62 or (resid 63 and (name N or name CA or name C or \ name O or name CB )) or resid 64 through 68 or resid 77 through 82 or (resid 83 \ through 84 and (name N or name CA or name C or name O or name CB )) or resid 85 \ or (resid 86 through 88 and (name N or name CA or name C or name O or name CB ) \ ) or resid 89 through 104 or (resid 105 through 106 and (name N or name CA or na \ me C or name O or name CB )) or (resid 107 through 113 and (name N or name CA or \ name C or name O or name CB )) or (resid 116 through 121 and (name N or name CA \ or name C or name O or name CB )) or resid 122 through 123 or (resid 124 throug \ h 130 and (name N or name CA or name C or name O or name CB )) or resid 131 thro \ ugh 143 or resid 156 through 190 or (resid 191 and (name N or name CA or name C \ or name O or name CB )) or resid 192 through 194 or (resid 195 through 196 and ( \ name N or name CA or name C or name O or name CB )) or resid 199 or (resid 200 a \ nd (name N or name CA or name C or name O or name CB )) or resid 201 or (resid 2 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 203 through \ 205 or (resid 206 through 208 and (name N or name CA or name C or name O or nam \ e CB )) or resid 209 through 222 or (resid 223 through 224 and (name N or name C \ A or name C or name O or name CB )) or resid 225 or (resid 226 through 229 and ( \ name N or name CA or name C or name O or name CB )) or resid 230 through 235 or \ (resid 236 through 264 and (name N or name CA or name C or name O or name CB )) \ or resid 265 through 270 or (resid 271 and (name N or name CA or name C or name \ O or name CB )) or resid 272 or (resid 273 and (name N or name CA or name C or n \ ame O or name CB )) or resid 274 through 285 or (resid 286 through 288 and (name \ N or name CA or name C or name O or name CB )) or resid 289 through 297 or (res \ id 298 and (name N or name CA or name C or name O or name CB )) or resid 299 thr \ ough 307 or (resid 308 through 309 and (name N or name CA or name C or name O or \ name CB )) or resid 310 through 535 or (resid 536 through 537 and (name N or na \ me CA or name C or name O or name CB )) or resid 538 through 546 or (resid 547 a \ nd (name N or name CA or name C or name O or name CB )) or resid 548 through 585 \ or (resid 586 through 588 and (name N or name CA or name C or name O or name CB \ )) or resid 589 through 591 or (resid 592 and (name N or name CA or name C or n \ ame O or name CB )) or resid 593 through 614 or (resid 615 and (name N or name C \ A or name C or name O or name CB )) or resid 616 through 674 or (resid 675 throu \ gh 691 and (name N or name CA or name C or name O or name CB )) or resid 692 thr \ ough 701 or (resid 702 and (name N or name CA or name C or name O or name CB )) \ or resid 703 through 707 or (resid 708 and (name N or name CA or name C or name \ O or name CB )) or resid 709 through 758 or (resid 759 and (name N or name CA or \ name C or name O or name CB )) or resid 760 through 785 or (resid 786 and (name \ N or name CA or name C or name O or name CB )) or resid 787 through 854 or (res \ id 855 and (name N or name CA or name C or name O or name CB )) or resid 856 thr \ ough 936 or (resid 937 and (name N or name CA or name C or name O or name CB )) \ or resid 938 through 966 or (resid 967 through 968 and (name N or name CA or nam \ e C or name O or name CB )) or resid 969 through 973 or (resid 974 and (name N o \ r name CA or name C or name O or name CB )) or resid 975 through 978 or (resid 9 \ 79 through 980 and (name N or name CA or name C or name O or name CB )) or resid \ 981 through 982 or (resid 983 through 986 and (name N or name CA or name C or n \ ame O or name CB )) or resid 987 or (resid 988 through 991 and (name N or name C \ A or name C or name O or name CB )) or resid 992 through 994 or (resid 995 and ( \ name N or name CA or name C or name O or name CB )) or resid 996 through 1044 or \ (resid 1045 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 046 through 1083 or (resid 1084 and (name N or name CA or name C or name O or na \ me CB )) or resid 1085 through 1117 or (resid 1118 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1119 through 1126 or (resid 1127 and (name \ N or name CA or name C or name O or name CB )) or resid 1128 through 1141 or (re \ sid 1142 and (name N or name CA or name C or name O or name CB )) or resid 1143 \ or (resid 1144 through 1145 and (name N or name CA or name C or name O or name C \ B )) or resid 9301 through 9316)) selection = (chain 'C' and (resid 14 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 94 or (resid 95 through 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 266 or ( \ resid 267 and (name N or name CA or name C or name O or name CB )) or resid 268 \ through 277 or (resid 278 and (name N or name CA or name C or name O or name CB \ )) or resid 279 or (resid 280 through 281 and (name N or name CA or name C or na \ me O or name CB )) or resid 282 through 285 or (resid 286 through 288 and (name \ N or name CA or name C or name O or name CB )) or resid 289 through 297 or (resi \ d 298 and (name N or name CA or name C or name O or name CB )) or resid 299 thro \ ugh 303 or (resid 304 through 305 and (name N or name CA or name C or name O or \ name CB )) or resid 306 through 316 or (resid 317 and (name N or name CA or name \ C or name O or name CB )) or resid 318 through 327 or (resid 328 through 329 an \ d (name N or name CA or name C or name O or name CB )) or resid 330 through 334 \ or (resid 335 and (name N or name CA or name C or name O or name CB )) or resid \ 336 through 539 or (resid 540 through 544 and (name N or name CA or name C or na \ me O or name CB )) or resid 545 through 575 or (resid 576 and (name N or name CA \ or name C or name O or name CB )) or resid 577 through 579 or (resid 580 throug \ h 588 and (name N or name CA or name C or name O or name CB )) or resid 589 thro \ ugh 644 or (resid 645 and (name N or name CA or name C or name O or name CB )) o \ r resid 646 through 658 or (resid 659 and (name N or name CA or name C or name O \ or name CB )) or resid 660 through 676 or (resid 689 through 691 and (name N or \ name CA or name C or name O or name CB )) or resid 692 through 710 or (resid 71 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 712 through \ 720 or (resid 721 and (name N or name CA or name C or name O or name CB )) or re \ sid 722 through 750 or (resid 751 and (name N or name CA or name C or name O or \ name CB )) or resid 752 through 784 or (resid 785 through 786 and (name N or nam \ e CA or name C or name O or name CB )) or resid 787 through 826 or (resid 850 th \ rough 852 and (name N or name CA or name C or name O or name CB )) or resid 853 \ or (resid 854 through 855 and (name N or name CA or name C or name O or name CB \ )) or resid 856 through 867 or (resid 868 and (name N or name CA or name C or na \ me O or name CB )) or resid 869 through 936 or (resid 937 and (name N or name CA \ or name C or name O or name CB )) or resid 938 through 966 or (resid 967 throug \ h 968 and (name N or name CA or name C or name O or name CB )) or resid 969 thro \ ugh 972 or (resid 973 through 974 and (name N or name CA or name C or name O or \ name CB )) or resid 975 through 978 or (resid 979 through 980 and (name N or nam \ e CA or name C or name O or name CB )) or resid 981 through 982 or (resid 983 th \ rough 986 and (name N or name CA or name C or name O or name CB )) or resid 987 \ through 1091 or (resid 1092 and (name N or name CA or name C or name O or name C \ B )) or resid 1093 through 1099 or (resid 1100 and (name N or name CA or name C \ or name O or name CB )) or resid 1101 through 1117 or (resid 1118 and (name N or \ name CA or name C or name O or name CB )) or resid 1119 through 1145 or resid 9 \ 301 through 9316)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 1 through 126) selection = (chain 'N' and resid 1 through 126) } ncs_group { reference = chain 'K' selection = chain 'M' selection = (chain 'O' and (resid 2 through 11 or resid 15 through 105)) } 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 individual isotropic 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: 5.680 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: 27.710 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 84.650 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.250 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 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 : 0.010 0.086 28400 Z= 0.655 Angle : 1.371 10.545 39067 Z= 0.947 Chirality : 0.081 1.363 4906 Planarity : 0.005 0.042 5272 Dihedral : 8.595 89.442 9223 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.17 % Allowed : 0.64 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.12), residues: 4297 helix: 0.16 (0.19), residues: 683 sheet: 1.06 (0.13), residues: 1319 loop : 0.21 (0.12), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP B 64 HIS 0.002 0.001 HIS A1048 PHE 0.013 0.002 PHE A 898 TYR 0.033 0.004 TYR B 269 ARG 0.004 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 327 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 ASN cc_start: 0.8011 (t0) cc_final: 0.7676 (t0) REVERT: A 613 GLN cc_start: 0.8612 (mt0) cc_final: 0.8367 (mt0) REVERT: C 337 PRO cc_start: 0.6761 (Cg_endo) cc_final: 0.6543 (Cg_exo) outliers start: 3 outliers final: 1 residues processed: 330 average time/residue: 0.3692 time to fit residues: 193.0313 Evaluate side-chains 174 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 165 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 367 optimal weight: 0.6980 chunk 329 optimal weight: 6.9990 chunk 182 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 222 optimal weight: 0.6980 chunk 176 optimal weight: 0.6980 chunk 340 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 253 optimal weight: 0.8980 chunk 395 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN B 314 GLN B1005 GLN C 314 GLN C 762 GLN C 907 ASN C 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28400 Z= 0.205 Angle : 0.557 10.290 39067 Z= 0.297 Chirality : 0.047 0.406 4906 Planarity : 0.004 0.052 5272 Dihedral : 4.747 55.783 5580 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.04 % Allowed : 4.47 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.12), residues: 4297 helix: 1.54 (0.20), residues: 688 sheet: 1.19 (0.14), residues: 1226 loop : 0.24 (0.12), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1102 HIS 0.005 0.001 HIS C1064 PHE 0.025 0.002 PHE C 981 TYR 0.022 0.002 TYR A 265 ARG 0.005 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 197 time to evaluate : 2.742 Fit side-chains revert: symmetry clash REVERT: A 544 ASN cc_start: 0.7990 (t0) cc_final: 0.7640 (t0) REVERT: C 337 PRO cc_start: 0.6954 (Cg_endo) cc_final: 0.6672 (Cg_exo) outliers start: 18 outliers final: 12 residues processed: 211 average time/residue: 0.3581 time to fit residues: 126.7699 Evaluate side-chains 169 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 219 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 328 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 395 optimal weight: 50.0000 chunk 427 optimal weight: 50.0000 chunk 352 optimal weight: 0.0020 chunk 392 optimal weight: 50.0000 chunk 134 optimal weight: 50.0000 chunk 317 optimal weight: 0.0970 overall best weight: 2.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B1005 GLN C 314 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 907 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 28400 Z= 0.435 Angle : 0.611 10.039 39067 Z= 0.321 Chirality : 0.050 0.385 4906 Planarity : 0.005 0.049 5272 Dihedral : 4.664 55.276 5580 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.63 % Allowed : 5.63 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.12), residues: 4297 helix: 1.22 (0.20), residues: 693 sheet: 1.17 (0.14), residues: 1271 loop : -0.00 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 886 HIS 0.010 0.003 HIS A1058 PHE 0.025 0.002 PHE C 92 TYR 0.027 0.002 TYR A1067 ARG 0.006 0.001 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 177 time to evaluate : 3.178 Fit side-chains revert: symmetry clash REVERT: A 607 GLN cc_start: 0.7580 (mt0) cc_final: 0.7309 (mt0) REVERT: A 750 SER cc_start: 0.8252 (t) cc_final: 0.7958 (m) REVERT: A 804 GLN cc_start: 0.8376 (mm-40) cc_final: 0.7956 (mm-40) REVERT: B 651 ILE cc_start: 0.8646 (mm) cc_final: 0.8403 (mt) REVERT: B 675 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.5962 (mp10) outliers start: 28 outliers final: 19 residues processed: 200 average time/residue: 0.3390 time to fit residues: 116.5747 Evaluate side-chains 186 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain H residue 23 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 390 optimal weight: 50.0000 chunk 297 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 43 optimal weight: 50.0000 chunk 188 optimal weight: 0.6980 chunk 265 optimal weight: 0.6980 chunk 397 optimal weight: 50.0000 chunk 420 optimal weight: 40.0000 chunk 207 optimal weight: 8.9990 chunk 376 optimal weight: 50.0000 chunk 113 optimal weight: 20.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN A1135 ASN B 314 GLN B1005 GLN C 314 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 935 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.140 28400 Z= 0.689 Angle : 0.753 13.777 39067 Z= 0.393 Chirality : 0.057 0.523 4906 Planarity : 0.006 0.069 5272 Dihedral : 5.691 59.661 5580 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.26 % Allowed : 7.60 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.12), residues: 4297 helix: 0.49 (0.20), residues: 678 sheet: 0.82 (0.14), residues: 1275 loop : -0.44 (0.12), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 886 HIS 0.022 0.004 HIS A1058 PHE 0.032 0.003 PHE C 92 TYR 0.030 0.003 TYR A1067 ARG 0.008 0.001 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 173 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 750 SER cc_start: 0.8299 (t) cc_final: 0.7993 (m) REVERT: A 786 LYS cc_start: 0.7948 (mmtm) cc_final: 0.7405 (mmmt) REVERT: A 804 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7960 (mm-40) REVERT: B 651 ILE cc_start: 0.8683 (mm) cc_final: 0.8444 (mt) REVERT: B 675 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6149 (mp10) REVERT: C 937 SER cc_start: 0.7793 (t) cc_final: 0.7410 (m) REVERT: C 1113 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7522 (mt0) outliers start: 39 outliers final: 28 residues processed: 204 average time/residue: 0.3493 time to fit residues: 121.4633 Evaluate side-chains 190 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 350 optimal weight: 30.0000 chunk 238 optimal weight: 30.0000 chunk 6 optimal weight: 0.7980 chunk 313 optimal weight: 40.0000 chunk 173 optimal weight: 1.9990 chunk 358 optimal weight: 0.8980 chunk 290 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 214 optimal weight: 20.0000 chunk 377 optimal weight: 50.0000 chunk 106 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 GLN A 957 GLN B 641 ASN B 762 GLN C 314 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28400 Z= 0.229 Angle : 0.529 9.153 39067 Z= 0.275 Chirality : 0.047 0.364 4906 Planarity : 0.004 0.061 5272 Dihedral : 4.928 58.573 5580 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.28 % Allowed : 9.23 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.13), residues: 4297 helix: 1.31 (0.20), residues: 670 sheet: 0.98 (0.14), residues: 1248 loop : -0.29 (0.12), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 886 HIS 0.005 0.001 HIS A1058 PHE 0.019 0.001 PHE C 541 TYR 0.022 0.001 TYR C 265 ARG 0.002 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 750 SER cc_start: 0.8192 (t) cc_final: 0.7959 (m) REVERT: A 804 GLN cc_start: 0.8303 (mm-40) cc_final: 0.8084 (mm-40) REVERT: B 651 ILE cc_start: 0.8652 (mm) cc_final: 0.8400 (mt) REVERT: B 675 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6009 (mp10) REVERT: C 779 GLN cc_start: 0.8158 (tt0) cc_final: 0.7946 (tp40) REVERT: C 937 SER cc_start: 0.7700 (t) cc_final: 0.7346 (m) outliers start: 22 outliers final: 16 residues processed: 179 average time/residue: 0.3440 time to fit residues: 107.9330 Evaluate side-chains 172 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 141 optimal weight: 2.9990 chunk 378 optimal weight: 50.0000 chunk 83 optimal weight: 0.9990 chunk 246 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 420 optimal weight: 30.0000 chunk 349 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 139 optimal weight: 50.0000 chunk 220 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 957 GLN B 641 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.124 28400 Z= 0.528 Angle : 0.649 10.477 39067 Z= 0.336 Chirality : 0.052 0.413 4906 Planarity : 0.005 0.058 5272 Dihedral : 5.271 59.664 5580 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.15 % Allowed : 9.00 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.13), residues: 4297 helix: 0.91 (0.20), residues: 674 sheet: 0.82 (0.14), residues: 1249 loop : -0.45 (0.12), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 886 HIS 0.012 0.002 HIS A1058 PHE 0.028 0.002 PHE A 392 TYR 0.027 0.002 TYR A 265 ARG 0.004 0.001 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 162 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 750 SER cc_start: 0.8224 (t) cc_final: 0.8005 (m) REVERT: A 804 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8028 (mm-40) REVERT: B 318 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7344 (t80) REVERT: B 651 ILE cc_start: 0.8711 (mm) cc_final: 0.8485 (mt) REVERT: B 675 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6103 (mp10) REVERT: C 937 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.7493 (m) REVERT: C 1113 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7474 (mt0) outliers start: 37 outliers final: 24 residues processed: 190 average time/residue: 0.3155 time to fit residues: 103.6513 Evaluate side-chains 186 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 405 optimal weight: 50.0000 chunk 47 optimal weight: 1.9990 chunk 239 optimal weight: 30.0000 chunk 307 optimal weight: 0.0030 chunk 238 optimal weight: 30.0000 chunk 354 optimal weight: 7.9990 chunk 235 optimal weight: 30.0000 chunk 419 optimal weight: 0.8980 chunk 262 optimal weight: 0.6980 chunk 255 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C 992 GLN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28400 Z= 0.176 Angle : 0.502 8.485 39067 Z= 0.260 Chirality : 0.046 0.408 4906 Planarity : 0.004 0.045 5272 Dihedral : 4.637 56.105 5580 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.57 % Allowed : 9.75 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.13), residues: 4297 helix: 1.64 (0.21), residues: 656 sheet: 0.94 (0.14), residues: 1241 loop : -0.27 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 886 HIS 0.003 0.001 HIS A1058 PHE 0.022 0.001 PHE A 392 TYR 0.019 0.001 TYR C 265 ARG 0.002 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 853 GLN cc_start: 0.7107 (mt0) cc_final: 0.6586 (pp30) REVERT: B 318 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.7250 (t80) REVERT: B 651 ILE cc_start: 0.8663 (mm) cc_final: 0.8408 (mt) REVERT: B 675 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6026 (mp10) REVERT: C 1113 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7285 (mt0) outliers start: 27 outliers final: 17 residues processed: 191 average time/residue: 0.3383 time to fit residues: 111.1455 Evaluate side-chains 179 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 259 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 250 optimal weight: 6.9990 chunk 126 optimal weight: 0.0870 chunk 82 optimal weight: 1.9990 chunk 81 optimal weight: 0.0060 chunk 266 optimal weight: 0.9980 chunk 285 optimal weight: 0.7980 chunk 207 optimal weight: 20.0000 chunk 39 optimal weight: 50.0000 chunk 329 optimal weight: 30.0000 overall best weight: 0.7776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 804 GLN A 957 GLN B 641 ASN B1005 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28400 Z= 0.192 Angle : 0.498 8.532 39067 Z= 0.256 Chirality : 0.046 0.381 4906 Planarity : 0.004 0.042 5272 Dihedral : 4.364 56.079 5580 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.63 % Allowed : 9.87 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.13), residues: 4297 helix: 1.87 (0.21), residues: 658 sheet: 0.99 (0.14), residues: 1278 loop : -0.20 (0.13), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.004 0.001 HIS A1058 PHE 0.020 0.001 PHE C 541 TYR 0.021 0.001 TYR C 265 ARG 0.002 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 853 GLN cc_start: 0.7081 (mt0) cc_final: 0.6583 (pp30) REVERT: B 318 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7226 (t80) REVERT: B 651 ILE cc_start: 0.8676 (mm) cc_final: 0.8425 (mt) REVERT: B 675 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6090 (mp10) REVERT: C 1113 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7314 (mt0) outliers start: 28 outliers final: 22 residues processed: 189 average time/residue: 0.3564 time to fit residues: 114.7298 Evaluate side-chains 182 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** 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 306, in __init__ self.caller(self.refine_xyz) 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 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.3738 > 50: distance: 6 - 9: 22.076 distance: 9 - 10: 18.437 distance: 10 - 11: 18.841 distance: 10 - 13: 50.521 distance: 11 - 12: 16.054 distance: 11 - 14: 19.815 distance: 14 - 15: 18.073 distance: 15 - 16: 23.618 distance: 15 - 18: 16.951 distance: 16 - 17: 38.073 distance: 16 - 19: 21.405 distance: 19 - 20: 11.805 distance: 20 - 21: 33.336 distance: 20 - 23: 34.956 distance: 21 - 22: 31.593 distance: 21 - 24: 21.792 distance: 24 - 25: 19.101 distance: 25 - 26: 5.580 distance: 25 - 28: 30.375 distance: 26 - 27: 22.196 distance: 26 - 29: 12.387 distance: 29 - 30: 13.261 distance: 29 - 151: 13.472 distance: 30 - 31: 5.471 distance: 30 - 33: 8.589 distance: 31 - 32: 8.243 distance: 31 - 34: 10.254 distance: 34 - 35: 7.457 distance: 35 - 36: 5.374 distance: 35 - 38: 6.181 distance: 36 - 37: 3.267 distance: 39 - 141: 3.103 distance: 41 - 42: 5.030 distance: 44 - 45: 15.838 distance: 44 - 85: 4.059 distance: 45 - 46: 32.244 distance: 45 - 48: 16.177 distance: 46 - 47: 33.145 distance: 46 - 49: 29.414 distance: 47 - 82: 13.252 distance: 49 - 50: 29.132 distance: 49 - 131: 21.329 distance: 50 - 51: 27.042 distance: 50 - 53: 11.648 distance: 51 - 52: 33.135 distance: 51 - 54: 4.605 distance: 52 - 128: 10.700 distance: 54 - 55: 9.685 distance: 55 - 56: 24.248 distance: 55 - 58: 42.559 distance: 56 - 57: 13.457 distance: 56 - 59: 11.672