Starting phenix.real_space_refine on Fri Mar 22 13:13:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly2_23582/03_2024/7ly2_23582.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly2_23582/03_2024/7ly2_23582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly2_23582/03_2024/7ly2_23582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly2_23582/03_2024/7ly2_23582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly2_23582/03_2024/7ly2_23582.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly2_23582/03_2024/7ly2_23582.pdb" } resolution = 2.5 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= 0.005 sd= 0.126 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 153 5.16 5 C 21183 2.51 5 N 5541 2.21 5 O 6567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "F ARG 98": "NH1" <-> "NH2" Residue "J PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 191": "OE1" <-> "OE2" Residue "J GLU 298": "OE1" <-> "OE2" Residue "J TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 773": "OE1" <-> "OE2" Residue "J ARG 815": "NH1" <-> "NH2" Residue "J GLU 868": "OE1" <-> "OE2" Residue "J GLU 988": "OE1" <-> "OE2" Residue "M ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33444 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 7994 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 56, 'TRANS': 984} Chain breaks: 8 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 768 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 578 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 487 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 9, 'ASN:plan1': 3, 'TRP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 240 Chain: "L" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 535 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 5, 'TYR:plan': 7, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "B" Number of atoms: 7994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 7994 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 56, 'TRANS': 984} Chain breaks: 8 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 768 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 578 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 487 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 9, 'ASN:plan1': 3, 'TRP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 240 Chain: "I" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 535 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 5, 'TYR:plan': 7, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "J" Number of atoms: 7994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 7994 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 56, 'TRANS': 984} Chain breaks: 8 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 95 Chain: "K" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 768 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 578 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 487 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 9, 'ASN:plan1': 3, 'TRP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 240 Chain: "O" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 535 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 5, 'TYR:plan': 7, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" 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: "R" 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: "S" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" 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: "U" 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: "V" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" 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: "X" 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: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "J" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 19.22, per 1000 atoms: 0.57 Number of scatterers: 33444 At special positions: 0 Unit cell: (204.75, 190.05, 191.1, 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 153 16.00 O 6567 8.00 N 5541 7.00 C 21183 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.13 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.10 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.11 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.06 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.13 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.10 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.11 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.06 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 87 " distance=2.04 Simple disulfide: pdb=" SG CYS J 15 " - pdb=" SG CYS J 136 " distance=2.04 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 166 " distance=2.04 Simple disulfide: pdb=" SG CYS J 291 " - pdb=" SG CYS J 301 " distance=2.02 Simple disulfide: pdb=" SG CYS J 336 " - pdb=" SG CYS J 361 " distance=2.02 Simple disulfide: pdb=" SG CYS J 379 " - pdb=" SG CYS J 432 " distance=2.13 Simple disulfide: pdb=" SG CYS J 391 " - pdb=" SG CYS J 525 " distance=2.05 Simple disulfide: pdb=" SG CYS J 480 " - pdb=" SG CYS J 488 " distance=2.03 Simple disulfide: pdb=" SG CYS J 538 " - pdb=" SG CYS J 590 " distance=2.02 Simple disulfide: pdb=" SG CYS J 617 " - pdb=" SG CYS J 649 " distance=2.04 Simple disulfide: pdb=" SG CYS J 662 " - pdb=" SG CYS J 671 " distance=2.03 Simple disulfide: pdb=" SG CYS J 738 " - pdb=" SG CYS J 760 " distance=2.11 Simple disulfide: pdb=" SG CYS J 743 " - pdb=" SG CYS J 749 " distance=2.11 Simple disulfide: pdb=" SG CYS J1032 " - pdb=" SG CYS J1043 " distance=2.01 Simple disulfide: pdb=" SG CYS J1082 " - pdb=" SG CYS J1126 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.06 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 87 " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG P 1 " - " FUC P 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 4 " " NAG V 1 " - " FUC V 4 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 149 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A1098 " " NAG A1313 " - " ASN A1134 " " NAG A1314 " - " ASN A 61 " " NAG A1315 " - " ASN A 234 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 149 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B1098 " " NAG B1313 " - " ASN B1134 " " NAG B1314 " - " ASN B 61 " " NAG B1315 " - " ASN B 234 " " NAG J1301 " - " ASN J 17 " " NAG J1302 " - " ASN J 122 " " NAG J1303 " - " ASN J 165 " " NAG J1304 " - " ASN J 282 " " NAG J1305 " - " ASN J 149 " " NAG J1306 " - " ASN J 331 " " NAG J1307 " - " ASN J 603 " " NAG J1308 " - " ASN J 616 " " NAG J1309 " - " ASN J 657 " " NAG J1310 " - " ASN J 709 " " NAG J1311 " - " ASN J1074 " " NAG J1312 " - " ASN J1098 " " NAG J1313 " - " ASN J1134 " " NAG J1314 " - " ASN J 61 " " NAG J1315 " - " ASN J 234 " " NAG P 1 " - " ASN A 343 " " NAG Q 1 " - " ASN A 717 " " NAG R 1 " - " ASN A 801 " " NAG S 1 " - " ASN B 343 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN J 343 " " NAG W 1 " - " ASN J 717 " " NAG X 1 " - " ASN J 801 " Time building additional restraints: 13.64 Conformation dependent library (CDL) restraints added in 6.3 seconds 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8274 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 84 sheets defined 21.1% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.77 Creating SS restraints... Processing helix chain 'A' and resid 247 through 250 removed outlier: 3.806A pdb=" N THR A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 250' 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: 3.604A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.178A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.726A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.733A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.055A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 976 through 984 Processing helix chain 'A' and resid 985 through 1031 removed outlier: 4.818A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.571A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.524A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'B' and resid 247 through 250 removed outlier: 3.807A pdb=" N THR B 250 " --> pdb=" O SER B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 250' 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: 3.604A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.178A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.726A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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: 3.733A 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 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.055A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 1031 removed outlier: 4.818A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.571A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.525A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 25 through 29 Processing helix chain 'I' and resid 78 through 82 Processing helix chain 'J' and resid 247 through 250 removed outlier: 3.807A pdb=" N THR J 250 " --> pdb=" O SER J 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 247 through 250' Processing helix chain 'J' and resid 294 through 303 Processing helix chain 'J' and resid 338 through 343 Processing helix chain 'J' and resid 349 through 353 removed outlier: 3.604A pdb=" N TRP J 353 " --> pdb=" O VAL J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 370 Processing helix chain 'J' and resid 386 through 389 Processing helix chain 'J' and resid 405 through 410 removed outlier: 4.178A pdb=" N ARG J 408 " --> pdb=" O ASP J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 422 Processing helix chain 'J' and resid 502 through 505 Processing helix chain 'J' and resid 616 through 620 removed outlier: 3.726A pdb=" N VAL J 620 " --> pdb=" O CYS J 617 " (cutoff:3.500A) Processing helix chain 'J' and resid 737 through 744 Processing helix chain 'J' and resid 746 through 754 Processing helix chain 'J' and resid 755 through 757 No H-bonds generated for 'chain 'J' and resid 755 through 757' Processing helix chain 'J' and resid 758 through 783 removed outlier: 3.733A pdb=" N ASP J 775 " --> pdb=" O ALA J 771 " (cutoff:3.500A) Processing helix chain 'J' and resid 816 through 826 Processing helix chain 'J' and resid 853 through 856 Processing helix chain 'J' and resid 866 through 885 Processing helix chain 'J' and resid 886 through 890 Processing helix chain 'J' and resid 897 through 908 Processing helix chain 'J' and resid 912 through 919 removed outlier: 4.055A pdb=" N LEU J 916 " --> pdb=" O THR J 912 " (cutoff:3.500A) Processing helix chain 'J' and resid 919 through 940 Processing helix chain 'J' and resid 941 through 944 Processing helix chain 'J' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL J 951 " --> pdb=" O LYS J 947 " (cutoff:3.500A) Processing helix chain 'J' and resid 966 through 968 No H-bonds generated for 'chain 'J' and resid 966 through 968' Processing helix chain 'J' and resid 976 through 984 Processing helix chain 'J' and resid 985 through 1031 removed outlier: 4.818A pdb=" N VAL J 991 " --> pdb=" O PRO J 987 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.571A pdb=" N PHE K 84 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.525A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'O' and resid 25 through 29 Processing helix chain 'O' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.050A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.913A 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: 3.707A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.984A 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: 12.470A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.416A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.315A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.617A 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: 5.257A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.986A 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: 6.266A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 565 " --> pdb=" O PHE J 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.763A 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: 6.578A 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 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.562A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.646A pdb=" N ALA A 701 " --> pdb=" O ILE J 788 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LYS J 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASN A 703 " --> pdb=" O LYS J 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.483A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.483A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.428A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.795A pdb=" N LYS A 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.777A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.501A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.501A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.690A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.690A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR E 114 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.715A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.060A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.472A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.472A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AD4, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.050A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.707A pdb=" N ALA J 575 " --> pdb=" O GLY J 566 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASP J 574 " --> pdb=" O ILE J 587 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU J 324 " --> pdb=" O ASN J 540 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ASN J 542 " --> pdb=" O GLU J 324 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE J 326 " --> pdb=" O ASN J 542 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.984A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.470A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.416A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.315A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.258A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.763A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.578A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.561A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.483A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.483A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.428A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 787 through 790 removed outlier: 3.795A pdb=" N LYS B 790 " --> pdb=" O ASN J 703 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.777A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.500A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TYR C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.500A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TYR C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.690A pdb=" N GLU F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.690A pdb=" N GLU F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR F 114 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.715A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.060A pdb=" N TYR G 108 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 9 through 11 removed outlier: 6.471A pdb=" N VAL I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP I 34 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 9 through 11 removed outlier: 6.471A pdb=" N VAL I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AG5, first strand: chain 'J' and resid 28 through 30 removed outlier: 8.049A pdb=" N ASN J 61 " --> pdb=" O TYR J 269 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR J 269 " --> pdb=" O ASN J 61 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA J 264 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR J 95 " --> pdb=" O ALA J 264 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE J 201 " --> pdb=" O ASP J 228 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP J 228 " --> pdb=" O PHE J 201 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE J 203 " --> pdb=" O LEU J 226 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 47 through 55 removed outlier: 3.984A pdb=" N ASP J 287 " --> pdb=" O LYS J 278 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 84 through 85 removed outlier: 12.470A pdb=" N PHE J 135 " --> pdb=" O PHE J 238 " (cutoff:3.500A) removed outlier: 12.416A pdb=" N THR J 240 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N ASN J 137 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N LEU J 242 " --> pdb=" O ASN J 137 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU J 244 " --> pdb=" O PRO J 139 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU J 141 " --> pdb=" O LEU J 244 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N CYS J 136 " --> pdb=" O SER J 161 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER J 161 " --> pdb=" O CYS J 136 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP J 138 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL J 159 " --> pdb=" O ASP J 138 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE J 140 " --> pdb=" O PHE J 157 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE J 157 " --> pdb=" O PHE J 140 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY J 142 " --> pdb=" O SER J 155 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 84 through 85 removed outlier: 6.315A pdb=" N ALA J 243 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE J 101 " --> pdb=" O ALA J 243 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ARG J 102 " --> pdb=" O ASN J 121 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE J 168 " --> pdb=" O VAL J 130 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 311 through 319 removed outlier: 5.257A pdb=" N ILE J 312 " --> pdb=" O THR J 599 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR J 599 " --> pdb=" O ILE J 312 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLN J 314 " --> pdb=" O VAL J 597 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL J 597 " --> pdb=" O GLN J 314 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY J 594 " --> pdb=" O GLN J 613 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 354 through 358 removed outlier: 3.763A pdb=" N ASN J 394 " --> pdb=" O GLU J 516 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 361 through 362 removed outlier: 6.578A pdb=" N CYS J 361 " --> pdb=" O CYS J 525 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 452 through 454 Processing sheet with id=AH4, first strand: chain 'J' and resid 473 through 474 Processing sheet with id=AH5, first strand: chain 'J' and resid 654 through 655 removed outlier: 6.561A pdb=" N ILE J 670 " --> pdb=" O ILE J 666 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 711 through 728 removed outlier: 6.483A pdb=" N SER J 711 " --> pdb=" O THR J1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR J1076 " --> pdb=" O SER J 711 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA J 713 " --> pdb=" O ASN J1074 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASN J1074 " --> pdb=" O ALA J 713 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU J1072 " --> pdb=" O PRO J 715 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR J1067 " --> pdb=" O HIS J1048 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS J1048 " --> pdb=" O TYR J1067 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 711 through 728 removed outlier: 6.483A pdb=" N SER J 711 " --> pdb=" O THR J1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR J1076 " --> pdb=" O SER J 711 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA J 713 " --> pdb=" O ASN J1074 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASN J1074 " --> pdb=" O ALA J 713 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU J1072 " --> pdb=" O PRO J 715 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE J1095 " --> pdb=" O ALA J1078 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 733 through 736 removed outlier: 4.428A pdb=" N LYS J 733 " --> pdb=" O LEU J 861 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 1120 through 1125 removed outlier: 4.778A pdb=" N ALA J1087 " --> pdb=" O SER J1123 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AI2, first strand: chain 'K' and resid 54 through 55 removed outlier: 6.501A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 54 through 55 removed outlier: 6.501A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AI5, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.690A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.690A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR M 114 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AI8, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.715A pdb=" N MET N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 11 through 12 removed outlier: 4.060A pdb=" N TYR N 108 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'O' and resid 9 through 11 removed outlier: 6.471A pdb=" N VAL O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP O 34 " --> pdb=" O VAL O 46 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'O' and resid 9 through 11 removed outlier: 6.471A pdb=" N VAL O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'O' and resid 18 through 23 1586 hydrogen bonds defined for protein. 4020 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: 20.38 Time building geometry restraints manager: 14.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8130 1.33 - 1.46: 9368 1.46 - 1.58: 16471 1.58 - 1.71: 0 1.71 - 1.84: 198 Bond restraints: 34167 Sorted by residual: bond pdb=" N GLU A 619 " pdb=" CA GLU A 619 " ideal model delta sigma weight residual 1.455 1.501 -0.046 1.37e-02 5.33e+03 1.14e+01 bond pdb=" N GLU J 619 " pdb=" CA GLU J 619 " ideal model delta sigma weight residual 1.455 1.501 -0.046 1.37e-02 5.33e+03 1.13e+01 bond pdb=" N GLU B 619 " pdb=" CA GLU B 619 " ideal model delta sigma weight residual 1.455 1.501 -0.046 1.37e-02 5.33e+03 1.12e+01 bond pdb=" C5 NAG B1314 " pdb=" O5 NAG B1314 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.52e+00 bond pdb=" CG ASP C 83 " pdb=" OD2 ASP C 83 " ideal model delta sigma weight residual 1.249 1.197 0.052 1.90e-02 2.77e+03 7.42e+00 ... (remaining 34162 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.51: 1032 106.51 - 113.38: 18485 113.38 - 120.26: 11720 120.26 - 127.13: 15250 127.13 - 134.01: 178 Bond angle restraints: 46665 Sorted by residual: angle pdb=" C GLN O 6 " pdb=" N PRO O 7 " pdb=" CA PRO O 7 " ideal model delta sigma weight residual 119.66 125.99 -6.33 7.30e-01 1.88e+00 7.52e+01 angle pdb=" C GLN I 6 " pdb=" N PRO I 7 " pdb=" CA PRO I 7 " ideal model delta sigma weight residual 119.66 125.98 -6.32 7.30e-01 1.88e+00 7.51e+01 angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 125.98 -6.32 7.30e-01 1.88e+00 7.50e+01 angle pdb=" C THR J 791 " pdb=" N PRO J 792 " pdb=" CA PRO J 792 " ideal model delta sigma weight residual 119.66 125.84 -6.18 7.20e-01 1.93e+00 7.37e+01 angle pdb=" C THR B 791 " pdb=" N PRO B 792 " pdb=" CA PRO B 792 " ideal model delta sigma weight residual 119.66 125.81 -6.15 7.20e-01 1.93e+00 7.29e+01 ... (remaining 46660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.31: 20334 21.31 - 42.63: 540 42.63 - 63.94: 117 63.94 - 85.25: 48 85.25 - 106.57: 18 Dihedral angle restraints: 21057 sinusoidal: 8160 harmonic: 12897 Sorted by residual: dihedral pdb=" C ASN B 616 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " pdb=" CB ASN B 616 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" C ASN A 616 " pdb=" N ASN A 616 " pdb=" CA ASN A 616 " pdb=" CB ASN A 616 " ideal model delta harmonic sigma weight residual -122.60 -136.32 13.72 0 2.50e+00 1.60e-01 3.01e+01 dihedral pdb=" C ASN J 616 " pdb=" N ASN J 616 " pdb=" CA ASN J 616 " pdb=" CB ASN J 616 " ideal model delta harmonic sigma weight residual -122.60 -136.32 13.72 0 2.50e+00 1.60e-01 3.01e+01 ... (remaining 21054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 4418 0.082 - 0.164: 845 0.164 - 0.245: 215 0.245 - 0.327: 66 0.327 - 0.409: 6 Chirality restraints: 5550 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.66e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.61e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.61e+01 ... (remaining 5547 not shown) Planarity restraints: 6072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 92 " -0.041 2.00e-02 2.50e+03 2.11e-02 8.89e+00 pdb=" CG TYR D 92 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR D 92 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR D 92 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR D 92 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 92 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR D 92 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 92 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 92 " 0.040 2.00e-02 2.50e+03 2.09e-02 8.76e+00 pdb=" CG TYR K 92 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR K 92 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR K 92 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR K 92 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR K 92 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR K 92 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR K 92 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 92 " 0.040 2.00e-02 2.50e+03 2.09e-02 8.74e+00 pdb=" CG TYR C 92 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR C 92 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR C 92 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR C 92 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 92 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR C 92 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 92 " 0.028 2.00e-02 2.50e+03 ... (remaining 6069 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 14720 2.92 - 3.42: 29784 3.42 - 3.91: 57829 3.91 - 4.41: 64870 4.41 - 4.90: 107136 Nonbonded interactions: 274339 Sorted by model distance: nonbonded pdb=" OD1 ASN B 331 " pdb=" O5 NAG B1306 " model vdw 2.427 3.040 nonbonded pdb=" OD1 ASN J 331 " pdb=" O5 NAG J1306 " model vdw 2.427 3.040 nonbonded pdb=" OD1 ASN A 331 " pdb=" O5 NAG A1306 " model vdw 2.427 3.040 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.437 2.520 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.437 2.520 ... (remaining 274334 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' } 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: 2.670 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: 14.220 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 98.960 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 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 : 0.011 0.061 34167 Z= 0.725 Angle : 1.237 12.162 46665 Z= 0.839 Chirality : 0.075 0.409 5550 Planarity : 0.005 0.027 6018 Dihedral : 11.258 106.565 12621 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.19 % Allowed : 0.75 % Favored : 99.06 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.33 % 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: 0.74 (0.12), residues: 4392 helix: 0.46 (0.19), residues: 669 sheet: 0.75 (0.13), residues: 1314 loop : 0.49 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP E 106 HIS 0.006 0.001 HIS B1048 PHE 0.020 0.003 PHE A 898 TYR 0.041 0.005 TYR D 92 ARG 0.003 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 637 time to evaluate : 3.324 Fit side-chains REVERT: A 29 THR cc_start: 0.7968 (t) cc_final: 0.7659 (p) REVERT: A 369 TYR cc_start: 0.8494 (t80) cc_final: 0.8259 (t80) REVERT: A 755 GLN cc_start: 0.8253 (mt0) cc_final: 0.8004 (mt0) REVERT: E 34 MET cc_start: 0.8392 (tpp) cc_final: 0.7854 (tpp) REVERT: E 48 MET cc_start: 0.8258 (mtp) cc_final: 0.8018 (mtm) REVERT: E 93 VAL cc_start: 0.7936 (t) cc_final: 0.7731 (p) REVERT: B 227 VAL cc_start: 0.8109 (p) cc_final: 0.7841 (m) REVERT: B 369 TYR cc_start: 0.8548 (t80) cc_final: 0.8338 (t80) REVERT: B 725 GLU cc_start: 0.7358 (tt0) cc_final: 0.6929 (tm-30) REVERT: B 755 GLN cc_start: 0.8245 (mt0) cc_final: 0.7948 (mt0) REVERT: B 1029 MET cc_start: 0.8738 (tpp) cc_final: 0.8454 (tpp) REVERT: C 103 THR cc_start: 0.7482 (p) cc_final: 0.7072 (t) REVERT: F 34 MET cc_start: 0.8398 (tpp) cc_final: 0.8099 (tpp) REVERT: F 70 MET cc_start: 0.8330 (mtt) cc_final: 0.8097 (mtt) REVERT: F 95 TYR cc_start: 0.8565 (m-80) cc_final: 0.8285 (m-80) REVERT: J 29 THR cc_start: 0.7957 (t) cc_final: 0.7576 (p) REVERT: J 318 PHE cc_start: 0.7675 (t80) cc_final: 0.7430 (t80) REVERT: J 523 THR cc_start: 0.8347 (p) cc_final: 0.8128 (p) REVERT: J 1050 MET cc_start: 0.8914 (ptm) cc_final: 0.8645 (ptp) REVERT: K 103 THR cc_start: 0.7434 (p) cc_final: 0.7109 (t) outliers start: 6 outliers final: 0 residues processed: 642 average time/residue: 1.4199 time to fit residues: 1089.2086 Evaluate side-chains 398 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 372 optimal weight: 0.6980 chunk 334 optimal weight: 0.6980 chunk 185 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 225 optimal weight: 0.5980 chunk 178 optimal weight: 0.7980 chunk 345 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 210 optimal weight: 0.7980 chunk 257 optimal weight: 0.7980 chunk 400 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 271 GLN A 394 ASN A 440 ASN A 641 ASN A 644 GLN A 675 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN D 38 GLN B 52 GLN B 81 ASN B 271 GLN B 394 ASN B 540 ASN B 580 GLN B 644 GLN B 779 GLN B 804 GLN B 957 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 ASN J 394 ASN J 580 GLN J 644 GLN J 675 GLN J 762 GLN J 804 GLN ** J1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1113 GLN K 38 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34167 Z= 0.204 Angle : 0.568 9.858 46665 Z= 0.301 Chirality : 0.045 0.248 5550 Planarity : 0.004 0.036 6018 Dihedral : 6.780 71.349 6171 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 2.01 % Allowed : 8.03 % Favored : 89.97 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.33 % 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: 1.41 (0.12), residues: 4392 helix: 2.16 (0.21), residues: 627 sheet: 0.96 (0.14), residues: 1260 loop : 0.75 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 36 HIS 0.007 0.001 HIS A 207 PHE 0.014 0.002 PHE A 898 TYR 0.024 0.002 TYR J1067 ARG 0.003 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 445 time to evaluate : 3.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ARG cc_start: 0.7551 (mmm160) cc_final: 0.7299 (mtp180) REVERT: A 725 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7042 (tm-30) REVERT: A 755 GLN cc_start: 0.8275 (mt0) cc_final: 0.8023 (mt0) REVERT: A 1010 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7484 (mp10) REVERT: E 34 MET cc_start: 0.8313 (tpp) cc_final: 0.7875 (tpp) REVERT: E 48 MET cc_start: 0.8343 (mtp) cc_final: 0.8121 (mtm) REVERT: B 725 GLU cc_start: 0.7399 (tt0) cc_final: 0.7049 (tm-30) REVERT: B 755 GLN cc_start: 0.8261 (mt0) cc_final: 0.7919 (mt0) REVERT: B 787 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7290 (mt0) REVERT: B 1017 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7332 (tm-30) REVERT: B 1029 MET cc_start: 0.8787 (tpp) cc_final: 0.8495 (tpp) REVERT: B 1050 MET cc_start: 0.8737 (ptm) cc_final: 0.8493 (ptp) REVERT: C 103 THR cc_start: 0.7701 (p) cc_final: 0.7447 (t) REVERT: F 34 MET cc_start: 0.8352 (tpp) cc_final: 0.8061 (tpp) REVERT: F 95 TYR cc_start: 0.8618 (m-80) cc_final: 0.8388 (m-80) REVERT: J 523 THR cc_start: 0.8394 (p) cc_final: 0.8193 (p) REVERT: J 814 LYS cc_start: 0.6467 (OUTLIER) cc_final: 0.5889 (mtmt) REVERT: J 1050 MET cc_start: 0.8736 (ptm) cc_final: 0.8496 (ptp) REVERT: K 103 THR cc_start: 0.7583 (p) cc_final: 0.7317 (t) REVERT: M 87 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.6103 (mtp180) outliers start: 64 outliers final: 21 residues processed: 481 average time/residue: 1.3216 time to fit residues: 767.3730 Evaluate side-chains 412 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 386 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain J residue 394 ASN Chi-restraints excluded: chain J residue 591 SER Chi-restraints excluded: chain J residue 814 LYS Chi-restraints excluded: chain J residue 821 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain M residue 87 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 70.8908 > 50: distance: 32 - 36: 27.514 distance: 37 - 40: 46.744 distance: 38 - 39: 18.967 distance: 38 - 45: 47.153 distance: 40 - 41: 40.574 distance: 41 - 42: 39.964 distance: 42 - 44: 10.490 distance: 45 - 46: 5.820 distance: 46 - 47: 26.831 distance: 46 - 49: 19.569 distance: 47 - 48: 37.307 distance: 47 - 52: 35.489 distance: 49 - 50: 12.775 distance: 52 - 174: 34.817 distance: 53 - 56: 41.280 distance: 54 - 55: 38.694 distance: 54 - 58: 25.499 distance: 55 - 171: 30.919 distance: 58 - 59: 14.597 distance: 59 - 62: 19.210 distance: 60 - 66: 20.299 distance: 62 - 63: 26.324 distance: 63 - 64: 20.311 distance: 63 - 65: 41.133 distance: 66 - 67: 43.915 distance: 66 - 166: 28.818 distance: 67 - 68: 32.819 distance: 67 - 70: 17.771 distance: 68 - 69: 29.212 distance: 68 - 77: 65.335 distance: 69 - 163: 27.099 distance: 70 - 71: 17.931 distance: 71 - 72: 18.048 distance: 71 - 73: 40.788 distance: 72 - 74: 13.023 distance: 73 - 75: 13.100 distance: 74 - 76: 19.006 distance: 75 - 76: 21.563 distance: 77 - 78: 16.477 distance: 78 - 79: 21.839 distance: 78 - 81: 39.378 distance: 79 - 80: 41.193 distance: 79 - 88: 56.137 distance: 81 - 82: 39.549 distance: 82 - 83: 9.097 distance: 83 - 84: 29.233 distance: 84 - 85: 29.885 distance: 85 - 86: 42.020 distance: 85 - 87: 63.285 distance: 88 - 89: 54.386 distance: 89 - 90: 49.299 distance: 89 - 92: 46.917 distance: 90 - 91: 40.069 distance: 92 - 94: 40.248 distance: 95 - 96: 40.912 distance: 96 - 99: 49.692 distance: 97 - 98: 23.261 distance: 97 - 104: 40.195 distance: 99 - 100: 11.694 distance: 100 - 101: 39.225 distance: 101 - 102: 40.709 distance: 101 - 103: 49.260 distance: 104 - 110: 29.597 distance: 105 - 106: 40.507 distance: 105 - 108: 39.929 distance: 106 - 107: 5.398 distance: 106 - 111: 39.161 distance: 108 - 109: 40.448 distance: 109 - 110: 41.457 distance: 111 - 112: 40.160 distance: 112 - 113: 40.259 distance: 112 - 115: 39.841 distance: 113 - 118: 34.295 distance: 115 - 116: 41.876 distance: 115 - 117: 40.184