Starting phenix.real_space_refine on Tue Aug 26 02:58:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n8h_24236/08_2025/7n8h_24236.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n8h_24236/08_2025/7n8h_24236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n8h_24236/08_2025/7n8h_24236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n8h_24236/08_2025/7n8h_24236.map" model { file = "/net/cci-nas-00/data/ceres_data/7n8h_24236/08_2025/7n8h_24236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n8h_24236/08_2025/7n8h_24236.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.107 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 144 5.16 5 C 20319 2.51 5 N 5382 2.21 5 O 7076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32921 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 7603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7603 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 3, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 751 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 953 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 538 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'TRP:plan': 2, 'GLN:plan1': 8, 'ASP:plan': 7, 'ARG:plan': 3, 'PHE:plan': 7, 'TYR:plan': 5, 'ASN:plan1': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 180 Chain: "C" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 596 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 5, 'ARG:plan': 7, 'PHE:plan': 4, 'ASN:plan1': 5, 'TYR:plan': 11, 'HIS:plan': 1, 'TRP:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 237 Chain: "F" Number of atoms: 7603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7603 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 3, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "G" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 751 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 953 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 538 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'TRP:plan': 2, 'GLN:plan1': 8, 'ASP:plan': 7, 'ARG:plan': 3, 'PHE:plan': 7, 'TYR:plan': 5, 'ASN:plan1': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 180 Chain: "J" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 596 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 5, 'ARG:plan': 7, 'PHE:plan': 4, 'ASN:plan1': 5, 'TYR:plan': 11, 'HIS:plan': 1, 'TRP:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 237 Chain: "K" Number of atoms: 7603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7603 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 3, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "L" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 751 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "M" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 953 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 538 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'TRP:plan': 2, 'GLN:plan1': 8, 'ASP:plan': 7, 'ARG:plan': 3, 'PHE:plan': 7, 'TYR:plan': 5, 'ASN:plan1': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 180 Chain: "O" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 596 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 5, 'ARG:plan': 7, 'PHE:plan': 4, 'ASN:plan1': 5, 'TYR:plan': 11, 'HIS:plan': 1, 'TRP:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 237 Chain: "P" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "F" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "K" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 181 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 13 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 240 Classifications: {'water': 240} Link IDs: {None: 239} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 240 Classifications: {'water': 240} Link IDs: {None: 239} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "K" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 240 Classifications: {'water': 240} Link IDs: {None: 239} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 8.00, per 1000 atoms: 0.24 Number of scatterers: 32921 At special positions: 0 Unit cell: (144.996, 149.211, 192.204, 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 144 16.00 O 7076 8.00 N 5382 7.00 C 20319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.18 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.07 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=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.11 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.12 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.14 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.10 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.05 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.02 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.18 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.07 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.01 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.11 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.12 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.04 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.14 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.10 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.05 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.02 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.05 Simple disulfide: pdb=" SG CYS K 291 " - pdb=" SG CYS K 301 " distance=2.03 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 361 " distance=2.02 Simple disulfide: pdb=" SG CYS K 379 " - pdb=" SG CYS K 432 " distance=2.18 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.07 Simple disulfide: pdb=" SG CYS K 480 " - pdb=" SG CYS K 488 " distance=2.03 Simple disulfide: pdb=" SG CYS K 538 " - pdb=" SG CYS K 590 " distance=2.01 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.11 Simple disulfide: pdb=" SG CYS K 662 " - pdb=" SG CYS K 671 " distance=2.12 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 760 " distance=2.03 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.14 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=2.03 Simple disulfide: pdb=" SG CYS K1082 " - pdb=" SG CYS K1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.10 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.05 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG P 1 " - " FUC P 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG V 1 " - " FUC V 3 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 709 " " NAG A1313 " - " ASN A 282 " " NAG F1301 " - " ASN F 122 " " NAG F1302 " - " ASN F 61 " " NAG F1303 " - " ASN F 234 " " NAG F1304 " - " ASN F 165 " " NAG F1305 " - " ASN F 331 " " NAG F1306 " - " ASN F 603 " " NAG F1307 " - " ASN F 657 " " NAG F1308 " - " ASN F1074 " " NAG F1309 " - " ASN F1098 " " NAG F1310 " - " ASN F1134 " " NAG F1311 " - " ASN F 616 " " NAG F1312 " - " ASN F 709 " " NAG F1313 " - " ASN F 282 " " NAG K1301 " - " ASN K 122 " " NAG K1302 " - " ASN K 61 " " NAG K1303 " - " ASN K 234 " " NAG K1304 " - " ASN K 165 " " NAG K1305 " - " ASN K 331 " " NAG K1308 " - " ASN K 603 " " NAG K1309 " - " ASN K 657 " " NAG K1314 " - " ASN K1074 " " NAG K1315 " - " ASN K1098 " " NAG K1316 " - " ASN K1134 " " NAG K1317 " - " ASN K 616 " " NAG K1318 " - " ASN K 709 " " NAG K1319 " - " ASN K 282 " " NAG P 1 " - " ASN A 343 " " NAG Q 1 " - " ASN A 717 " " NAG R 1 " - " ASN A 801 " " NAG S 1 " - " ASN F 343 " " NAG T 1 " - " ASN F 717 " " NAG U 1 " - " ASN F 801 " " NAG V 1 " - " ASN K 343 " " NAG W 1 " - " ASN K 717 " " NAG X 1 " - " ASN K 801 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 81 sheets defined 21.1% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.974A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.479A 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 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.737A 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: 3.785A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 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 891 removed outlier: 3.962A 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 912 through 919 removed outlier: 4.066A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.758A 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 1033 removed outlier: 3.723A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (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 'E' and resid 28 through 32 removed outlier: 3.610A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 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 'E' and resid 107 through 111 removed outlier: 3.869A pdb=" N TYR E 111 " --> pdb=" O GLY E 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.878A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'F' and resid 383 through 389 removed outlier: 4.974A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.479A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 502 through 505 Processing helix chain 'F' and resid 616 through 620 removed outlier: 3.737A pdb=" N VAL F 620 " --> pdb=" O CYS F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 744 Processing helix chain 'F' and resid 746 through 754 Processing helix chain 'F' and resid 755 through 757 No H-bonds generated for 'chain 'F' and resid 755 through 757' Processing helix chain 'F' and resid 758 through 783 removed outlier: 3.785A pdb=" N ASP F 775 " --> pdb=" O ALA F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 824 Processing helix chain 'F' and resid 853 through 856 Processing helix chain 'F' and resid 866 through 885 Processing helix chain 'F' and resid 886 through 891 removed outlier: 3.962A pdb=" N ALA F 890 " --> pdb=" O TRP F 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 908 Processing helix chain 'F' and resid 912 through 919 removed outlier: 4.066A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 939 Processing helix chain 'F' and resid 945 through 965 removed outlier: 3.758A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) Processing helix chain 'F' and resid 966 through 968 No H-bonds generated for 'chain 'F' and resid 966 through 968' Processing helix chain 'F' and resid 976 through 984 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 3.723A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.610A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.870A pdb=" N TYR H 111 " --> pdb=" O GLY H 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.878A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 294 through 304 Processing helix chain 'K' and resid 338 through 343 Processing helix chain 'K' and resid 365 through 370 Processing helix chain 'K' and resid 383 through 389 removed outlier: 4.974A pdb=" N ASN K 388 " --> pdb=" O THR K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 removed outlier: 4.479A pdb=" N ARG K 408 " --> pdb=" O ASP K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 422 Processing helix chain 'K' and resid 438 through 443 Processing helix chain 'K' and resid 502 through 505 Processing helix chain 'K' and resid 616 through 620 removed outlier: 3.737A pdb=" N VAL K 620 " --> pdb=" O CYS K 617 " (cutoff:3.500A) Processing helix chain 'K' and resid 737 through 744 Processing helix chain 'K' and resid 746 through 754 Processing helix chain 'K' and resid 755 through 757 No H-bonds generated for 'chain 'K' and resid 755 through 757' Processing helix chain 'K' and resid 758 through 783 removed outlier: 3.785A pdb=" N ASP K 775 " --> pdb=" O ALA K 771 " (cutoff:3.500A) Processing helix chain 'K' and resid 816 through 824 Processing helix chain 'K' and resid 853 through 856 Processing helix chain 'K' and resid 866 through 885 Processing helix chain 'K' and resid 886 through 891 removed outlier: 3.961A pdb=" N ALA K 890 " --> pdb=" O TRP K 886 " (cutoff:3.500A) Processing helix chain 'K' and resid 897 through 908 Processing helix chain 'K' and resid 912 through 919 removed outlier: 4.065A pdb=" N LEU K 916 " --> pdb=" O THR K 912 " (cutoff:3.500A) Processing helix chain 'K' and resid 919 through 939 Processing helix chain 'K' and resid 945 through 965 removed outlier: 3.758A pdb=" N VAL K 951 " --> pdb=" O LYS K 947 " (cutoff:3.500A) Processing helix chain 'K' and resid 966 through 968 No H-bonds generated for 'chain 'K' and resid 966 through 968' Processing helix chain 'K' and resid 976 through 984 Processing helix chain 'K' and resid 985 through 1033 removed outlier: 3.723A pdb=" N VAL K 991 " --> pdb=" O PRO K 987 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN K 992 " --> pdb=" O GLU K 988 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.610A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 65 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 'M' and resid 107 through 111 removed outlier: 3.870A pdb=" N TYR M 111 " --> pdb=" O GLY M 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.877A pdb=" N ILE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.883A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.970A 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: 3.771A pdb=" N ALA K 575 " --> pdb=" O GLY K 566 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP K 574 " --> pdb=" O ILE K 587 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU K 324 " --> pdb=" O ASN K 540 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASN K 542 " --> pdb=" O GLU K 324 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE K 326 " --> pdb=" O ASN K 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.425A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.626A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.224A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.294A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE A 565 " --> pdb=" O PHE F 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.701A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.590A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.640A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.640A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.508A 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: 4.306A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.784A pdb=" N ILE A 788 " --> pdb=" O ASN K 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.612A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 4 through 7 removed outlier: 5.615A pdb=" N THR D 70 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N GLN D 27 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N SER D 68 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N VAL D 29 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N SER D 66 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 54 through 55 removed outlier: 5.582A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 54 through 55 removed outlier: 5.582A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.560A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.560A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR E 114 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.915A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 67 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.383A pdb=" N LEU B 33 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.613A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.633A pdb=" N MET C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AD3, first strand: chain 'F' and resid 28 through 31 removed outlier: 3.883A pdb=" N SER F 60 " --> pdb=" O SER F 31 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE F 201 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP F 228 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE F 203 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 47 through 55 removed outlier: 7.425A pdb=" N THR F 274 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASP F 290 " --> pdb=" O THR F 274 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU F 276 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA F 288 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS F 278 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 84 through 85 removed outlier: 6.626A pdb=" N VAL F 126 " --> pdb=" O TYR F 170 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR F 170 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE F 128 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE F 168 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL F 130 " --> pdb=" O CYS F 166 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N CYS F 166 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER F 162 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 311 through 319 removed outlier: 5.224A pdb=" N ILE F 312 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR F 599 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN F 314 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL F 597 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER F 316 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 324 through 328 removed outlier: 6.293A pdb=" N GLU F 324 " --> pdb=" O ASN F 540 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASN F 542 " --> pdb=" O GLU F 324 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE F 326 " --> pdb=" O ASN F 542 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA F 575 " --> pdb=" O GLY F 566 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE F 565 " --> pdb=" O PHE K 43 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 354 through 358 Processing sheet with id=AD9, first strand: chain 'F' and resid 361 through 362 removed outlier: 6.701A pdb=" N CYS F 361 " --> pdb=" O CYS F 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.590A pdb=" N ILE F 670 " --> pdb=" O ILE F 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 702 through 704 Processing sheet with id=AE5, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.640A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.640A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA F1078 " --> pdb=" O PHE F1095 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE F1095 " --> pdb=" O ALA F1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.306A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 4.611A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 4 through 7 removed outlier: 5.615A pdb=" N THR G 70 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N GLN G 27 " --> pdb=" O SER G 68 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N SER G 68 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N VAL G 29 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N SER G 66 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 54 through 55 removed outlier: 5.582A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 54 through 55 removed outlier: 5.582A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.560A pdb=" N GLU H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.560A pdb=" N GLU H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.915A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER I 67 " --> pdb=" O ASP I 70 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.384A pdb=" N LEU I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.613A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.633A pdb=" N MET J 34 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AG3, first strand: chain 'K' and resid 28 through 31 removed outlier: 3.883A pdb=" N SER K 60 " --> pdb=" O SER K 31 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 47 through 55 removed outlier: 7.425A pdb=" N THR K 274 " --> pdb=" O ASP K 290 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASP K 290 " --> pdb=" O THR K 274 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU K 276 " --> pdb=" O ALA K 288 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA K 288 " --> pdb=" O LEU K 276 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS K 278 " --> pdb=" O THR K 286 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 84 through 85 removed outlier: 6.626A pdb=" N VAL K 126 " --> pdb=" O TYR K 170 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR K 170 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE K 128 " --> pdb=" O PHE K 168 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE K 168 " --> pdb=" O ILE K 128 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL K 130 " --> pdb=" O CYS K 166 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N CYS K 166 " --> pdb=" O VAL K 130 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER K 162 " --> pdb=" O GLN K 134 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 311 through 319 removed outlier: 5.223A pdb=" N ILE K 312 " --> pdb=" O THR K 599 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR K 599 " --> pdb=" O ILE K 312 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN K 314 " --> pdb=" O VAL K 597 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL K 597 " --> pdb=" O GLN K 314 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER K 316 " --> pdb=" O VAL K 595 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY K 594 " --> pdb=" O GLN K 613 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 354 through 358 Processing sheet with id=AG8, first strand: chain 'K' and resid 361 through 362 removed outlier: 6.701A pdb=" N CYS K 361 " --> pdb=" O CYS K 525 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 452 through 454 Processing sheet with id=AH1, first strand: chain 'K' and resid 473 through 474 Processing sheet with id=AH2, first strand: chain 'K' and resid 654 through 655 removed outlier: 6.590A pdb=" N ILE K 670 " --> pdb=" O ILE K 666 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.641A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR K1067 " --> pdb=" O HIS K1048 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS K1048 " --> pdb=" O TYR K1067 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.641A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA K1078 " --> pdb=" O PHE K1095 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE K1095 " --> pdb=" O ALA K1078 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 733 through 736 removed outlier: 4.306A pdb=" N LYS K 733 " --> pdb=" O LEU K 861 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 1120 through 1125 removed outlier: 4.611A pdb=" N ALA K1087 " --> pdb=" O SER K1123 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.615A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 54 through 55 removed outlier: 5.582A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 54 through 55 removed outlier: 5.582A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AI2, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.559A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.559A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR M 114 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.915A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER N 67 " --> pdb=" O ASP N 70 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.384A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.614A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AI8, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.633A pdb=" N MET O 34 " --> pdb=" O PHE O 50 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'O' and resid 10 through 12 1560 hydrogen bonds defined for protein. 3996 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: 10.15 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5784 1.32 - 1.45: 8668 1.45 - 1.57: 18148 1.57 - 1.70: 51 1.70 - 1.83: 186 Bond restraints: 32837 Sorted by residual: bond pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " ideal model delta sigma weight residual 1.439 1.570 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" C2 NAG V 1 " pdb=" N2 NAG V 1 " ideal model delta sigma weight residual 1.439 1.570 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" C2 NAG S 1 " pdb=" N2 NAG S 1 " ideal model delta sigma weight residual 1.439 1.570 -0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C4 NAG X 1 " pdb=" O4 NAG X 1 " ideal model delta sigma weight residual 1.409 1.299 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 NAG R 1 " pdb=" O4 NAG R 1 " ideal model delta sigma weight residual 1.409 1.299 0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 32832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 41135 1.99 - 3.99: 3033 3.99 - 5.98: 459 5.98 - 7.97: 239 7.97 - 9.96: 18 Bond angle restraints: 44884 Sorted by residual: angle pdb=" C THR A 791 " pdb=" N PRO A 792 " pdb=" CA PRO A 792 " ideal model delta sigma weight residual 119.66 126.20 -6.54 7.20e-01 1.93e+00 8.25e+01 angle pdb=" C THR K 791 " pdb=" N PRO K 792 " pdb=" CA PRO K 792 " ideal model delta sigma weight residual 119.66 126.17 -6.51 7.20e-01 1.93e+00 8.18e+01 angle pdb=" C THR F 791 " pdb=" N PRO F 792 " pdb=" CA PRO F 792 " ideal model delta sigma weight residual 119.66 126.16 -6.50 7.20e-01 1.93e+00 8.14e+01 angle pdb=" C LEU K 861 " pdb=" N PRO K 862 " pdb=" CA PRO K 862 " ideal model delta sigma weight residual 119.66 125.55 -5.89 7.20e-01 1.93e+00 6.69e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 125.55 -5.89 7.20e-01 1.93e+00 6.69e+01 ... (remaining 44879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 19369 17.96 - 35.92: 563 35.92 - 53.88: 141 53.88 - 71.85: 48 71.85 - 89.81: 33 Dihedral angle restraints: 20154 sinusoidal: 7593 harmonic: 12561 Sorted by residual: dihedral pdb=" CB CYS O 22 " pdb=" SG CYS O 22 " pdb=" SG CYS O 96 " pdb=" CB CYS O 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.29 41.71 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 96 " pdb=" CB CYS J 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.32 41.68 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.33 41.67 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 20151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4807 0.116 - 0.232: 426 0.232 - 0.347: 74 0.347 - 0.463: 21 0.463 - 0.579: 12 Chirality restraints: 5340 Sorted by residual: 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 -2.95 0.55 2.00e-02 2.50e+03 7.51e+02 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 -2.95 0.55 2.00e-02 2.50e+03 7.45e+02 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 -2.94 0.54 2.00e-02 2.50e+03 7.42e+02 ... (remaining 5337 not shown) Planarity restraints: 5874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " -0.046 2.00e-02 2.50e+03 4.69e-02 2.75e+01 pdb=" CG ASN A 165 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " 0.071 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 165 " 0.046 2.00e-02 2.50e+03 4.68e-02 2.74e+01 pdb=" CG ASN F 165 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN F 165 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN F 165 " -0.071 2.00e-02 2.50e+03 pdb=" C1 NAG F1304 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 165 " -0.046 2.00e-02 2.50e+03 4.67e-02 2.73e+01 pdb=" CG ASN K 165 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN K 165 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN K 165 " 0.071 2.00e-02 2.50e+03 pdb=" C1 NAG K1304 " -0.056 2.00e-02 2.50e+03 ... (remaining 5871 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 13824 2.91 - 3.41: 29272 3.41 - 3.90: 57161 3.90 - 4.40: 64378 4.40 - 4.90: 105121 Nonbonded interactions: 269756 Sorted by model distance: nonbonded pdb=" OE2 GLU K 406 " pdb=" O HOH K1401 " model vdw 2.409 3.040 nonbonded pdb=" OE2 GLU A 406 " pdb=" O HOH A1401 " model vdw 2.409 3.040 nonbonded pdb=" OE2 GLU F 406 " pdb=" O HOH F1401 " model vdw 2.410 3.040 nonbonded pdb=" OD2 ASP K 808 " pdb=" NZ LYS K 811 " model vdw 2.427 3.120 nonbonded pdb=" OD2 ASP F 808 " pdb=" NZ LYS F 811 " model vdw 2.427 3.120 ... (remaining 269751 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 1312 or (resid 1313 and (name C1 or name C2 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name N2 or nam \ e O3 or name O4 or name O5 or name O6 )))) selection = (chain 'F' and (resid 27 through 1312 or (resid 1313 and (name C1 or name C2 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name N2 or nam \ e O3 or name O4 or name O5 or name O6 )))) selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'M' } 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: 12.150 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: 0.470 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 35.010 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.140 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.013 0.252 32948 Z= 0.733 Angle : 1.284 9.964 45166 Z= 0.850 Chirality : 0.083 0.579 5340 Planarity : 0.006 0.035 5826 Dihedral : 10.700 89.808 11937 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.12), residues: 4284 helix: 0.31 (0.19), residues: 669 sheet: 0.95 (0.13), residues: 1368 loop : 0.25 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG F 237 TYR 0.058 0.006 TYR L 92 PHE 0.030 0.004 PHE K1075 TRP 0.027 0.005 TRP F 353 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01218 (32837) covalent geometry : angle 1.26288 (44884) SS BOND : bond 0.05755 ( 51) SS BOND : angle 3.50482 ( 102) hydrogen bonds : bond 0.17071 ( 1449) hydrogen bonds : angle 8.20255 ( 3996) link_BETA1-4 : bond 0.23863 ( 9) link_BETA1-4 : angle 3.19910 ( 27) link_BETA1-6 : bond 0.14675 ( 3) link_BETA1-6 : angle 3.45588 ( 9) link_NAG-ASN : bond 0.05122 ( 48) link_NAG-ASN : angle 2.88157 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 ASP cc_start: 0.8051 (t0) cc_final: 0.7823 (t70) REVERT: A 869 MET cc_start: 0.8975 (mtt) cc_final: 0.8399 (mtm) REVERT: A 902 MET cc_start: 0.8669 (tpp) cc_final: 0.8340 (tpp) REVERT: D 4 MET cc_start: 0.5810 (mmm) cc_final: 0.5230 (mmm) REVERT: E 38 ARG cc_start: 0.6353 (ttp-170) cc_final: 0.6137 (ttp-170) REVERT: G 4 MET cc_start: 0.5862 (mmm) cc_final: 0.5550 (mmm) REVERT: K 731 MET cc_start: 0.8236 (mtm) cc_final: 0.7922 (mtm) REVERT: K 902 MET cc_start: 0.8661 (tpp) cc_final: 0.8378 (tpp) REVERT: K 1050 MET cc_start: 0.8842 (ptm) cc_final: 0.8564 (ptm) outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 0.6691 time to fit residues: 423.0193 Evaluate side-chains 361 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 544 ASN A 901 GLN A1002 GLN A1058 HIS A1101 HIS F 394 ASN F 564 GLN F 613 GLN F 901 GLN F1002 GLN K 564 GLN K 607 GLN K 901 GLN K1002 GLN K1058 HIS K1101 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.211649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.187667 restraints weight = 27813.276| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 0.81 r_work: 0.3906 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 32948 Z= 0.168 Angle : 0.633 9.543 45166 Z= 0.335 Chirality : 0.048 0.172 5340 Planarity : 0.005 0.033 5826 Dihedral : 5.088 36.047 5859 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.93 % Allowed : 5.42 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.12), residues: 4284 helix: 1.69 (0.20), residues: 663 sheet: 1.03 (0.14), residues: 1332 loop : 0.23 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F1107 TYR 0.023 0.002 TYR F1067 PHE 0.014 0.002 PHE K1052 TRP 0.010 0.002 TRP F 886 HIS 0.010 0.002 HIS K1064 Details of bonding type rmsd covalent geometry : bond 0.00369 (32837) covalent geometry : angle 0.60948 (44884) SS BOND : bond 0.00439 ( 51) SS BOND : angle 1.13767 ( 102) hydrogen bonds : bond 0.05644 ( 1449) hydrogen bonds : angle 6.22710 ( 3996) link_BETA1-4 : bond 0.01015 ( 9) link_BETA1-4 : angle 1.96094 ( 27) link_BETA1-6 : bond 0.00176 ( 3) link_BETA1-6 : angle 1.94357 ( 9) link_NAG-ASN : bond 0.00741 ( 48) link_NAG-ASN : angle 2.81955 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 384 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 ASP cc_start: 0.8345 (t0) cc_final: 0.8129 (t70) REVERT: A 869 MET cc_start: 0.9127 (mtt) cc_final: 0.8675 (mtm) REVERT: A 902 MET cc_start: 0.8871 (tpp) cc_final: 0.8628 (tpp) REVERT: E 46 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6609 (tp30) REVERT: E 73 ASP cc_start: 0.7098 (t70) cc_final: 0.6841 (t70) REVERT: F 480 CYS cc_start: 0.6486 (m) cc_final: 0.6101 (m) REVERT: F 1050 MET cc_start: 0.8790 (ptm) cc_final: 0.8574 (ptm) REVERT: G 4 MET cc_start: 0.6203 (mmm) cc_final: 0.5899 (mmm) REVERT: H 46 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6451 (tp30) REVERT: K 590 CYS cc_start: 0.6997 (m) cc_final: 0.6766 (m) REVERT: K 780 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7516 (pp20) REVERT: K 1050 MET cc_start: 0.8873 (ptm) cc_final: 0.8471 (ptm) REVERT: M 46 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6460 (tp30) REVERT: M 73 ASP cc_start: 0.7168 (t70) cc_final: 0.6915 (t70) outliers start: 58 outliers final: 28 residues processed: 412 average time/residue: 0.5676 time to fit residues: 282.0648 Evaluate side-chains 382 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 350 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 994 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 483 VAL Chi-restraints excluded: chain K residue 780 GLU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 46 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 191 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 425 optimal weight: 40.0000 chunk 20 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 133 optimal weight: 0.1980 chunk 369 optimal weight: 2.9990 chunk 371 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 544 ASN A1101 HIS F 394 ASN K1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.210803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.188833 restraints weight = 27707.050| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 0.70 r_work: 0.3920 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32948 Z= 0.155 Angle : 0.588 8.832 45166 Z= 0.311 Chirality : 0.046 0.169 5340 Planarity : 0.004 0.058 5826 Dihedral : 4.815 35.885 5859 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.93 % Allowed : 6.35 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.12), residues: 4284 helix: 1.67 (0.20), residues: 672 sheet: 0.95 (0.14), residues: 1287 loop : 0.13 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 55 TYR 0.021 0.002 TYR F1067 PHE 0.015 0.002 PHE A 898 TRP 0.010 0.002 TRP E 106 HIS 0.006 0.002 HIS F1048 Details of bonding type rmsd covalent geometry : bond 0.00336 (32837) covalent geometry : angle 0.57174 (44884) SS BOND : bond 0.00397 ( 51) SS BOND : angle 1.52671 ( 102) hydrogen bonds : bond 0.05291 ( 1449) hydrogen bonds : angle 5.95739 ( 3996) link_BETA1-4 : bond 0.00891 ( 9) link_BETA1-4 : angle 1.96324 ( 27) link_BETA1-6 : bond 0.00021 ( 3) link_BETA1-6 : angle 1.66735 ( 9) link_NAG-ASN : bond 0.00627 ( 48) link_NAG-ASN : angle 1.96302 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 365 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.7567 (m-80) cc_final: 0.7196 (m-80) REVERT: A 663 ASP cc_start: 0.8304 (t0) cc_final: 0.8016 (t70) REVERT: A 869 MET cc_start: 0.9098 (mtt) cc_final: 0.8665 (mtm) REVERT: A 902 MET cc_start: 0.8808 (tpp) cc_final: 0.8586 (tpp) REVERT: E 46 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6604 (tp30) REVERT: E 73 ASP cc_start: 0.7053 (t70) cc_final: 0.6829 (t70) REVERT: F 528 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7369 (mttp) REVERT: F 1050 MET cc_start: 0.8786 (ptm) cc_final: 0.8564 (ptm) REVERT: H 46 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6391 (tp30) REVERT: H 73 ASP cc_start: 0.7181 (t70) cc_final: 0.6938 (t70) REVERT: K 194 PHE cc_start: 0.7554 (m-80) cc_final: 0.7119 (m-80) REVERT: K 590 CYS cc_start: 0.6963 (m) cc_final: 0.6720 (m) REVERT: K 780 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7451 (pp20) REVERT: K 1050 MET cc_start: 0.8883 (ptm) cc_final: 0.8447 (ptm) REVERT: M 46 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6435 (tp30) outliers start: 58 outliers final: 31 residues processed: 398 average time/residue: 0.6813 time to fit residues: 323.2294 Evaluate side-chains 378 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 342 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 528 LYS Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain F residue 994 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 528 LYS Chi-restraints excluded: chain K residue 780 GLU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 191 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 302 optimal weight: 0.0980 chunk 267 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 419 optimal weight: 0.0970 chunk 225 optimal weight: 0.0970 chunk 400 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 405 optimal weight: 3.9990 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 544 ASN A1101 HIS D 27 GLN F 394 ASN K1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.210701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.189708 restraints weight = 27627.984| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 0.71 r_work: 0.3933 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32948 Z= 0.148 Angle : 0.572 7.522 45166 Z= 0.302 Chirality : 0.046 0.209 5340 Planarity : 0.004 0.047 5826 Dihedral : 4.743 35.662 5859 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.16 % Allowed : 6.71 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.12), residues: 4284 helix: 1.74 (0.20), residues: 669 sheet: 0.96 (0.14), residues: 1266 loop : 0.05 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 905 TYR 0.021 0.002 TYR F1067 PHE 0.015 0.002 PHE A 898 TRP 0.011 0.002 TRP M 50 HIS 0.006 0.002 HIS F1048 Details of bonding type rmsd covalent geometry : bond 0.00322 (32837) covalent geometry : angle 0.55893 (44884) SS BOND : bond 0.00417 ( 51) SS BOND : angle 1.08937 ( 102) hydrogen bonds : bond 0.05069 ( 1449) hydrogen bonds : angle 5.76660 ( 3996) link_BETA1-4 : bond 0.00788 ( 9) link_BETA1-4 : angle 1.92052 ( 27) link_BETA1-6 : bond 0.00044 ( 3) link_BETA1-6 : angle 1.68899 ( 9) link_NAG-ASN : bond 0.00366 ( 48) link_NAG-ASN : angle 1.84899 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 359 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.7670 (m-80) cc_final: 0.7259 (m-80) REVERT: A 663 ASP cc_start: 0.8267 (t0) cc_final: 0.7970 (t70) REVERT: A 869 MET cc_start: 0.9077 (mtt) cc_final: 0.8560 (mtm) REVERT: F 528 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7357 (mttp) REVERT: F 820 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7471 (t0) REVERT: F 1050 MET cc_start: 0.8856 (ptm) cc_final: 0.8652 (ptm) REVERT: H 46 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6405 (tp30) REVERT: K 48 LEU cc_start: 0.8485 (mt) cc_final: 0.8283 (mp) REVERT: K 194 PHE cc_start: 0.7606 (m-80) cc_final: 0.7221 (m-80) REVERT: K 335 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.8026 (mp) REVERT: K 590 CYS cc_start: 0.7032 (m) cc_final: 0.6784 (m) REVERT: K 780 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7451 (pp20) REVERT: K 1050 MET cc_start: 0.8865 (ptm) cc_final: 0.8577 (ptm) REVERT: M 46 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6412 (tp30) REVERT: M 70 MET cc_start: 0.6892 (mtt) cc_final: 0.6596 (mtt) outliers start: 65 outliers final: 35 residues processed: 402 average time/residue: 0.6458 time to fit residues: 309.8278 Evaluate side-chains 385 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 344 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 528 LYS Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 820 ASP Chi-restraints excluded: chain F residue 994 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 528 LYS Chi-restraints excluded: chain K residue 780 GLU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 46 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 368 optimal weight: 4.9990 chunk 316 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 380 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 411 optimal weight: 9.9990 chunk 383 optimal weight: 0.7980 chunk 289 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 544 ASN A1101 HIS D 27 GLN F 394 ASN K 314 GLN K 613 GLN K1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.210640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.189073 restraints weight = 27651.927| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 0.74 r_work: 0.3934 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32948 Z= 0.139 Angle : 0.556 7.706 45166 Z= 0.292 Chirality : 0.046 0.256 5340 Planarity : 0.004 0.043 5826 Dihedral : 4.678 41.419 5859 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.16 % Allowed : 7.34 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.13), residues: 4284 helix: 1.77 (0.20), residues: 672 sheet: 1.01 (0.14), residues: 1293 loop : 0.03 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 905 TYR 0.020 0.002 TYR F1067 PHE 0.014 0.002 PHE A 898 TRP 0.011 0.002 TRP H 106 HIS 0.005 0.001 HIS F1048 Details of bonding type rmsd covalent geometry : bond 0.00302 (32837) covalent geometry : angle 0.54417 (44884) SS BOND : bond 0.00407 ( 51) SS BOND : angle 0.98055 ( 102) hydrogen bonds : bond 0.04885 ( 1449) hydrogen bonds : angle 5.65226 ( 3996) link_BETA1-4 : bond 0.00743 ( 9) link_BETA1-4 : angle 1.79317 ( 27) link_BETA1-6 : bond 0.00062 ( 3) link_BETA1-6 : angle 1.62151 ( 9) link_NAG-ASN : bond 0.00353 ( 48) link_NAG-ASN : angle 1.74716 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 352 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.7702 (m-80) cc_final: 0.7332 (m-80) REVERT: A 613 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7945 (mt0) REVERT: A 820 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7690 (t0) REVERT: A 869 MET cc_start: 0.9079 (mtt) cc_final: 0.8567 (mtm) REVERT: E 46 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6901 (tp30) REVERT: F 820 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7475 (t0) REVERT: F 1050 MET cc_start: 0.8813 (ptm) cc_final: 0.8603 (ptm) REVERT: H 46 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6396 (tp30) REVERT: H 70 MET cc_start: 0.7017 (mtt) cc_final: 0.6476 (mtt) REVERT: K 583 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6404 (tt0) REVERT: K 590 CYS cc_start: 0.7162 (m) cc_final: 0.6877 (m) REVERT: K 780 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7430 (pp20) REVERT: M 38 ARG cc_start: 0.6511 (ttp-170) cc_final: 0.6248 (ttp-170) REVERT: M 46 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6421 (tp30) REVERT: M 73 ASP cc_start: 0.7202 (t70) cc_final: 0.6890 (t70) outliers start: 65 outliers final: 36 residues processed: 395 average time/residue: 0.6241 time to fit residues: 295.3972 Evaluate side-chains 385 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 341 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 820 ASP Chi-restraints excluded: chain F residue 994 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 528 LYS Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 606 ASN Chi-restraints excluded: chain K residue 780 GLU Chi-restraints excluded: chain K residue 826 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 46 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 73 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 210 optimal weight: 0.0870 chunk 363 optimal weight: 0.5980 chunk 155 optimal weight: 6.9990 chunk 311 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 371 optimal weight: 5.9990 chunk 41 optimal weight: 0.0040 chunk 57 optimal weight: 0.8980 chunk 265 optimal weight: 20.0000 overall best weight: 0.5172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A1101 HIS D 27 GLN F 394 ASN K1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.212159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.191147 restraints weight = 27780.067| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 0.70 r_work: 0.3946 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32948 Z= 0.104 Angle : 0.512 10.222 45166 Z= 0.266 Chirality : 0.044 0.301 5340 Planarity : 0.004 0.044 5826 Dihedral : 4.438 42.796 5859 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.46 % Allowed : 8.44 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.13), residues: 4284 helix: 1.97 (0.20), residues: 669 sheet: 1.08 (0.14), residues: 1299 loop : 0.10 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F1091 TYR 0.020 0.001 TYR F1067 PHE 0.016 0.001 PHE M 64 TRP 0.010 0.001 TRP M 50 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00216 (32837) covalent geometry : angle 0.49798 (44884) SS BOND : bond 0.00299 ( 51) SS BOND : angle 0.84430 ( 102) hydrogen bonds : bond 0.04268 ( 1449) hydrogen bonds : angle 5.38805 ( 3996) link_BETA1-4 : bond 0.00712 ( 9) link_BETA1-4 : angle 1.55474 ( 27) link_BETA1-6 : bond 0.00165 ( 3) link_BETA1-6 : angle 1.54056 ( 9) link_NAG-ASN : bond 0.00305 ( 48) link_NAG-ASN : angle 1.97647 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 357 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.7688 (m-80) cc_final: 0.7352 (m-80) REVERT: A 820 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7654 (t0) REVERT: A 869 MET cc_start: 0.9054 (mtt) cc_final: 0.8611 (mtm) REVERT: F 820 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7467 (t0) REVERT: H 46 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6356 (tp30) REVERT: H 70 MET cc_start: 0.6944 (mtt) cc_final: 0.6266 (mtt) REVERT: K 590 CYS cc_start: 0.7184 (m) cc_final: 0.6924 (m) REVERT: M 46 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6412 (tp30) REVERT: M 77 THR cc_start: 0.7176 (p) cc_final: 0.6945 (m) outliers start: 44 outliers final: 29 residues processed: 386 average time/residue: 0.6699 time to fit residues: 308.7478 Evaluate side-chains 375 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 342 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 820 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 46 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 358 optimal weight: 0.6980 chunk 234 optimal weight: 4.9990 chunk 332 optimal weight: 5.9990 chunk 361 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 381 optimal weight: 0.8980 chunk 341 optimal weight: 5.9990 chunk 428 optimal weight: 30.0000 chunk 212 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 804 GLN A 935 GLN A1101 HIS D 27 GLN F 394 ASN K1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.210475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.189561 restraints weight = 27700.343| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 0.71 r_work: 0.3926 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3872 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32948 Z= 0.148 Angle : 0.573 9.245 45166 Z= 0.299 Chirality : 0.046 0.353 5340 Planarity : 0.004 0.035 5826 Dihedral : 4.727 44.889 5859 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.66 % Allowed : 8.64 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.13), residues: 4284 helix: 1.84 (0.20), residues: 669 sheet: 1.09 (0.14), residues: 1275 loop : 0.08 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 905 TYR 0.021 0.002 TYR F1067 PHE 0.016 0.002 PHE M 64 TRP 0.011 0.002 TRP E 106 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00324 (32837) covalent geometry : angle 0.55796 (44884) SS BOND : bond 0.00444 ( 51) SS BOND : angle 1.14712 ( 102) hydrogen bonds : bond 0.04985 ( 1449) hydrogen bonds : angle 5.59415 ( 3996) link_BETA1-4 : bond 0.00762 ( 9) link_BETA1-4 : angle 1.77319 ( 27) link_BETA1-6 : bond 0.00047 ( 3) link_BETA1-6 : angle 1.67822 ( 9) link_NAG-ASN : bond 0.00549 ( 48) link_NAG-ASN : angle 2.03488 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 351 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8451 (t0) cc_final: 0.8223 (t0) REVERT: A 820 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7755 (t0) REVERT: A 869 MET cc_start: 0.9089 (mtt) cc_final: 0.8612 (mtm) REVERT: F 820 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7527 (t0) REVERT: H 46 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6415 (tp30) REVERT: H 70 MET cc_start: 0.6972 (mtt) cc_final: 0.6329 (mtt) REVERT: K 335 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.8014 (mp) REVERT: K 528 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7412 (mttp) REVERT: K 590 CYS cc_start: 0.7224 (m) cc_final: 0.6956 (m) REVERT: K 663 ASP cc_start: 0.8166 (t0) cc_final: 0.7916 (t70) REVERT: M 46 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6413 (tp30) REVERT: M 70 MET cc_start: 0.6972 (mtt) cc_final: 0.6641 (mtt) REVERT: M 73 ASP cc_start: 0.7210 (t70) cc_final: 0.6829 (t70) outliers start: 50 outliers final: 34 residues processed: 387 average time/residue: 0.6344 time to fit residues: 294.0699 Evaluate side-chains 384 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 344 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 820 ASP Chi-restraints excluded: chain F residue 994 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 367 VAL Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 528 LYS Chi-restraints excluded: chain K residue 606 ASN Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 46 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 152 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 156 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 373 optimal weight: 0.5980 chunk 252 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 chunk 416 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 345 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A1101 HIS D 27 GLN F 394 ASN K1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.211328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.190286 restraints weight = 27731.640| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 0.71 r_work: 0.3935 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3889 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32948 Z= 0.120 Angle : 0.531 9.801 45166 Z= 0.276 Chirality : 0.045 0.267 5340 Planarity : 0.004 0.035 5826 Dihedral : 4.584 45.184 5859 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.30 % Allowed : 9.14 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.13), residues: 4284 helix: 1.93 (0.20), residues: 669 sheet: 1.17 (0.14), residues: 1266 loop : 0.11 (0.13), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 905 TYR 0.020 0.001 TYR F1067 PHE 0.016 0.001 PHE M 64 TRP 0.011 0.001 TRP M 50 HIS 0.005 0.001 HIS F1048 Details of bonding type rmsd covalent geometry : bond 0.00256 (32837) covalent geometry : angle 0.51728 (44884) SS BOND : bond 0.00345 ( 51) SS BOND : angle 1.01008 ( 102) hydrogen bonds : bond 0.04521 ( 1449) hydrogen bonds : angle 5.43389 ( 3996) link_BETA1-4 : bond 0.00733 ( 9) link_BETA1-4 : angle 1.57485 ( 27) link_BETA1-6 : bond 0.00082 ( 3) link_BETA1-6 : angle 1.57193 ( 9) link_NAG-ASN : bond 0.00458 ( 48) link_NAG-ASN : angle 1.91034 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 344 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8412 (t0) cc_final: 0.8207 (t0) REVERT: A 820 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7697 (t0) REVERT: A 869 MET cc_start: 0.9065 (mtt) cc_final: 0.8656 (mtm) REVERT: F 820 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7493 (t0) REVERT: H 46 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6382 (tp30) REVERT: H 70 MET cc_start: 0.6899 (mtt) cc_final: 0.6307 (mtt) REVERT: K 590 CYS cc_start: 0.7217 (m) cc_final: 0.6958 (m) REVERT: K 663 ASP cc_start: 0.7808 (t0) cc_final: 0.7564 (t0) REVERT: M 46 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6415 (tp30) REVERT: M 70 MET cc_start: 0.6941 (mtt) cc_final: 0.6611 (mtt) REVERT: M 73 ASP cc_start: 0.7237 (t70) cc_final: 0.6876 (t70) REVERT: M 77 THR cc_start: 0.7200 (p) cc_final: 0.6946 (m) outliers start: 39 outliers final: 29 residues processed: 371 average time/residue: 0.6466 time to fit residues: 286.3275 Evaluate side-chains 371 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 338 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 820 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 606 ASN Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 46 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 147 optimal weight: 5.9990 chunk 419 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 278 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 181 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 223 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN D 27 GLN F 394 ASN K1101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.210790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.189780 restraints weight = 27497.930| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 0.71 r_work: 0.3928 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32948 Z= 0.131 Angle : 0.548 10.054 45166 Z= 0.286 Chirality : 0.045 0.247 5340 Planarity : 0.004 0.034 5826 Dihedral : 4.668 46.141 5859 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.50 % Allowed : 9.04 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.13), residues: 4284 helix: 1.89 (0.20), residues: 669 sheet: 1.17 (0.14), residues: 1266 loop : 0.08 (0.13), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 905 TYR 0.020 0.002 TYR F1067 PHE 0.018 0.001 PHE M 64 TRP 0.011 0.001 TRP H 106 HIS 0.005 0.001 HIS F1048 Details of bonding type rmsd covalent geometry : bond 0.00285 (32837) covalent geometry : angle 0.53477 (44884) SS BOND : bond 0.00381 ( 51) SS BOND : angle 1.08050 ( 102) hydrogen bonds : bond 0.04729 ( 1449) hydrogen bonds : angle 5.48384 ( 3996) link_BETA1-4 : bond 0.00759 ( 9) link_BETA1-4 : angle 1.61148 ( 27) link_BETA1-6 : bond 0.00049 ( 3) link_BETA1-6 : angle 1.60489 ( 9) link_NAG-ASN : bond 0.00466 ( 48) link_NAG-ASN : angle 1.90058 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 343 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 820 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7748 (t0) REVERT: A 869 MET cc_start: 0.9080 (mtt) cc_final: 0.8575 (mtm) REVERT: A 979 ASP cc_start: 0.7834 (m-30) cc_final: 0.7266 (m-30) REVERT: E 46 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6871 (tp30) REVERT: F 820 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7498 (t0) REVERT: H 46 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6383 (tp30) REVERT: K 590 CYS cc_start: 0.7211 (m) cc_final: 0.6947 (m) REVERT: K 663 ASP cc_start: 0.7870 (t0) cc_final: 0.7651 (t0) REVERT: K 820 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7825 (t0) REVERT: M 46 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6405 (tp30) REVERT: M 70 MET cc_start: 0.6963 (mtt) cc_final: 0.6656 (mtt) REVERT: M 73 ASP cc_start: 0.7219 (t70) cc_final: 0.6852 (t70) outliers start: 45 outliers final: 32 residues processed: 374 average time/residue: 0.7406 time to fit residues: 330.6581 Evaluate side-chains 379 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 341 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 820 ASP Chi-restraints excluded: chain F residue 994 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 367 VAL Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 606 ASN Chi-restraints excluded: chain K residue 820 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 70 optimal weight: 4.9990 chunk 380 optimal weight: 0.6980 chunk 360 optimal weight: 0.8980 chunk 300 optimal weight: 4.9990 chunk 361 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 197 optimal weight: 0.0030 chunk 65 optimal weight: 0.8980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN F 394 ASN K1101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.211604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.190067 restraints weight = 27786.337| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 0.73 r_work: 0.3944 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32948 Z= 0.113 Angle : 0.526 10.076 45166 Z= 0.272 Chirality : 0.045 0.229 5340 Planarity : 0.004 0.034 5826 Dihedral : 4.567 46.150 5859 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.43 % Allowed : 9.27 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.13), residues: 4284 helix: 1.97 (0.20), residues: 669 sheet: 1.11 (0.14), residues: 1296 loop : 0.13 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F1107 TYR 0.020 0.001 TYR F1067 PHE 0.017 0.001 PHE M 64 TRP 0.011 0.001 TRP H 106 HIS 0.004 0.001 HIS F1048 Details of bonding type rmsd covalent geometry : bond 0.00240 (32837) covalent geometry : angle 0.51206 (44884) SS BOND : bond 0.00317 ( 51) SS BOND : angle 1.09977 ( 102) hydrogen bonds : bond 0.04407 ( 1449) hydrogen bonds : angle 5.35870 ( 3996) link_BETA1-4 : bond 0.00732 ( 9) link_BETA1-4 : angle 1.50288 ( 27) link_BETA1-6 : bond 0.00106 ( 3) link_BETA1-6 : angle 1.54522 ( 9) link_NAG-ASN : bond 0.00425 ( 48) link_NAG-ASN : angle 1.88316 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 348 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 820 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7726 (t0) REVERT: A 869 MET cc_start: 0.9055 (mtt) cc_final: 0.8634 (mtm) REVERT: E 38 ARG cc_start: 0.6494 (ttp-170) cc_final: 0.6278 (ttp-170) REVERT: E 46 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6882 (tp30) REVERT: E 70 MET cc_start: 0.6504 (mtt) cc_final: 0.6173 (mtp) REVERT: F 660 TYR cc_start: 0.8348 (m-80) cc_final: 0.8141 (m-80) REVERT: F 820 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7485 (t0) REVERT: H 46 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6383 (tp30) REVERT: H 70 MET cc_start: 0.6938 (mtt) cc_final: 0.6345 (mtt) REVERT: K 590 CYS cc_start: 0.7214 (m) cc_final: 0.6963 (m) REVERT: K 820 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7836 (t0) REVERT: M 46 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6408 (tp30) REVERT: M 70 MET cc_start: 0.6900 (mtt) cc_final: 0.6600 (mtt) REVERT: M 73 ASP cc_start: 0.7172 (t70) cc_final: 0.6858 (t70) REVERT: M 77 THR cc_start: 0.7166 (p) cc_final: 0.6952 (m) outliers start: 43 outliers final: 29 residues processed: 377 average time/residue: 0.7229 time to fit residues: 326.2637 Evaluate side-chains 375 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 340 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 820 ASP Chi-restraints excluded: chain F residue 994 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 606 ASN Chi-restraints excluded: chain K residue 820 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 246 optimal weight: 4.9990 chunk 366 optimal weight: 0.8980 chunk 423 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 403 optimal weight: 7.9990 chunk 210 optimal weight: 0.7980 chunk 312 optimal weight: 0.6980 chunk 387 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN D 27 GLN F 394 ASN F 804 GLN F 935 GLN K1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.210227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.188547 restraints weight = 27919.516| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 0.73 r_work: 0.3909 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32948 Z= 0.127 Angle : 0.548 11.771 45166 Z= 0.284 Chirality : 0.045 0.227 5340 Planarity : 0.004 0.034 5826 Dihedral : 4.656 45.994 5859 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.36 % Allowed : 9.41 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.13), residues: 4284 helix: 2.12 (0.20), residues: 651 sheet: 1.18 (0.14), residues: 1266 loop : 0.10 (0.13), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K1014 TYR 0.020 0.002 TYR F1067 PHE 0.018 0.001 PHE M 64 TRP 0.011 0.001 TRP H 106 HIS 0.004 0.001 HIS F1048 Details of bonding type rmsd covalent geometry : bond 0.00274 (32837) covalent geometry : angle 0.53336 (44884) SS BOND : bond 0.00366 ( 51) SS BOND : angle 1.26304 ( 102) hydrogen bonds : bond 0.04628 ( 1449) hydrogen bonds : angle 5.42574 ( 3996) link_BETA1-4 : bond 0.00732 ( 9) link_BETA1-4 : angle 1.54501 ( 27) link_BETA1-6 : bond 0.00083 ( 3) link_BETA1-6 : angle 1.59156 ( 9) link_NAG-ASN : bond 0.00448 ( 48) link_NAG-ASN : angle 1.97923 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12774.42 seconds wall clock time: 218 minutes 1.36 seconds (13081.36 seconds total)