Starting phenix.real_space_refine on Mon Jul 6 09:19:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lxz_23580/07_2026/7lxz_23580.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lxz_23580/07_2026/7lxz_23580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lxz_23580/07_2026/7lxz_23580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lxz_23580/07_2026/7lxz_23580.map" model { file = "/net/cci-nas-00/data/ceres_data/7lxz_23580/07_2026/7lxz_23580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lxz_23580/07_2026/7lxz_23580.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lxz_23580/07_2026/7lxz_23580.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lxz_23580/07_2026/7lxz_23580.cif" } resolution = 2.6 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= 0.005 sd= 0.120 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 21732 2.51 5 N 5739 2.21 5 O 6729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34353 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8197 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 58, 'TRANS': 1001} Chain breaks: 5 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 770 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 954 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 643 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 7, 'ARG:plan': 7, 'PHE:plan': 4, 'ASP:plan': 6, 'TYR:plan': 7, 'HIS:plan': 1, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 215 Chain: "J" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 534 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 149 Chain: "B" Number of atoms: 8197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8197 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 58, 'TRANS': 1001} Chain breaks: 5 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "C" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 770 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 954 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "G" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 643 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 7, 'ARG:plan': 7, 'PHE:plan': 4, 'ASP:plan': 6, 'TYR:plan': 7, 'HIS:plan': 1, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 215 Chain: "I" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 534 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 149 Chain: "K" Number of atoms: 8197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8197 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 58, 'TRANS': 1001} Chain breaks: 5 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "L" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 770 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 954 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 643 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 7, 'ARG:plan': 7, 'PHE:plan': 4, 'ASP:plan': 6, 'TYR:plan': 7, 'HIS:plan': 1, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 215 Chain: "O" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 534 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 149 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "S" 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 chiralities: 2 Chain: "T" 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 chiralities: 3 Chain: "U" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "V" 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 chiralities: 2 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 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 chiralities: 2 Chain: "Y" 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 chiralities: 3 Chain: "Z" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "a" 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 chiralities: 2 Chain: "b" 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 chiralities: 2 Chain: "c" 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 chiralities: 2 Chain: "d" 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 chiralities: 3 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 chiralities: 13 Chain: "B" 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 chiralities: 13 Chain: "K" 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 chiralities: 13 Time building chain proxies: 7.93, per 1000 atoms: 0.23 Number of scatterers: 34353 At special positions: 0 Unit cell: (194.25, 208.95, 191.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 153 16.00 O 6729 8.00 N 5739 7.00 C 21732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.14 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.09 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.08 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.09 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.01 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.14 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.09 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.08 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.09 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.01 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 136 " distance=2.02 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.03 Simple disulfide: pdb=" SG CYS K 291 " - pdb=" SG CYS K 301 " distance=2.02 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=2.14 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.10 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=2.02 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.04 Simple disulfide: pdb=" SG CYS K 662 " - pdb=" SG CYS K 671 " distance=2.04 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 760 " distance=2.08 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.09 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=2.02 Simple disulfide: pdb=" SG CYS K1082 " - pdb=" SG CYS K1126 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.01 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 P 2 " - " BMA P 3 " " 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 U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " BETA1-6 " NAG P 1 " - " FUC P 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG T 1 " - " FUC T 3 " " NAG U 1 " - " FUC U 4 " " NAG Y 1 " - " FUC Y 3 " " NAG Z 1 " - " FUC Z 4 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 122 " " NAG A1310 " - " ASN A 282 " " NAG A1311 " - " ASN A 234 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 61 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B 122 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B 234 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 61 " " NAG K1301 " - " ASN K 331 " " NAG K1302 " - " ASN K 603 " " NAG K1303 " - " ASN K 616 " " NAG K1304 " - " ASN K 657 " " NAG K1305 " - " ASN K 709 " " NAG K1306 " - " ASN K1074 " " NAG K1307 " - " ASN K1098 " " NAG K1308 " - " ASN K1134 " " NAG K1309 " - " ASN K 122 " " NAG K1310 " - " ASN K 282 " " NAG K1311 " - " ASN K 234 " " NAG K1312 " - " ASN K 165 " " NAG K1313 " - " ASN K 61 " " NAG P 1 " - " ASN A 343 " " NAG Q 1 " - " ASN A 717 " " NAG R 1 " - " ASN A 801 " " NAG S 1 " - " ASN A 149 " " NAG T 1 " - " ASN A 17 " " NAG U 1 " - " ASN B 343 " " NAG V 1 " - " ASN B 717 " " NAG W 1 " - " ASN B 801 " " NAG X 1 " - " ASN B 149 " " NAG Y 1 " - " ASN B 17 " " NAG Z 1 " - " ASN K 343 " " NAG a 1 " - " ASN K 717 " " NAG b 1 " - " ASN K 801 " " NAG c 1 " - " ASN K 149 " " NAG d 1 " - " ASN K 17 " Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.3 seconds 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8424 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 84 sheets defined 19.1% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.811A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.148A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 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: 3.727A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.083A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.925A 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: 4.782A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.565A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.566A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'J' and resid 81 through 85 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.810A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.148A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.727A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.084A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.925A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.782A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.565A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.566A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 81 through 85 Processing helix chain 'K' and resid 294 through 303 Processing helix chain 'K' and resid 338 through 343 Processing helix chain 'K' and resid 349 through 353 removed outlier: 3.811A pdb=" N TRP K 353 " --> pdb=" O VAL K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 370 Processing helix chain 'K' and resid 386 through 389 Processing helix chain 'K' and resid 405 through 410 removed outlier: 4.148A 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 502 through 505 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: 3.727A pdb=" N ASP K 775 " --> pdb=" O ALA K 771 " (cutoff:3.500A) Processing helix chain 'K' and resid 816 through 826 Processing helix chain 'K' and resid 866 through 885 Processing helix chain 'K' and resid 886 through 890 Processing helix chain 'K' and resid 897 through 908 Processing helix chain 'K' and resid 912 through 919 removed outlier: 4.083A pdb=" N LEU K 916 " --> pdb=" O THR K 912 " (cutoff:3.500A) Processing helix chain 'K' and resid 919 through 940 Processing helix chain 'K' and resid 945 through 965 removed outlier: 3.925A 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: 4.782A pdb=" N VAL K 991 " --> pdb=" O PRO K 987 " (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 'L' and resid 80 through 84 removed outlier: 3.565A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.567A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'O' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.057A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.733A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.389A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.502A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 12.798A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.271A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.259A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 565 " --> pdb=" O PHE K 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.885A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.552A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.549A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.659A pdb=" N ALA A 701 " --> pdb=" O ILE K 788 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS K 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASN A 703 " --> pdb=" O LYS K 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.414A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.513A pdb=" N LYS A 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.834A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 7 removed outlier: 5.544A pdb=" N THR D 70 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N GLN D 27 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N SER D 68 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 11.201A pdb=" N VAL D 29 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 11.299A pdb=" N SER D 66 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.488A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.488A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.760A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.760A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR E 114 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.919A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.692A pdb=" N TYR H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 9 through 11 removed outlier: 6.511A pdb=" N TRP J 37 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 9 through 11 Processing sheet with id=AD3, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AD4, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.057A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.734A pdb=" N ALA K 575 " --> pdb=" O GLY K 566 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP K 574 " --> pdb=" O ILE K 587 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU K 324 " --> pdb=" O ASN K 540 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASN K 542 " --> pdb=" O GLU K 324 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE K 326 " --> pdb=" O ASN K 542 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.388A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.501A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 83 through 85 removed outlier: 12.799A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.271A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.885A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.552A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.550A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.414A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 787 through 790 removed outlier: 3.513A pdb=" N LYS B 790 " --> pdb=" O ASN K 703 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.833A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 4 through 7 removed outlier: 5.544A pdb=" N THR C 70 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N GLN C 27 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 9.688A pdb=" N SER C 68 " --> pdb=" O GLN C 27 " (cutoff:3.500A) removed outlier: 11.202A pdb=" N VAL C 29 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 11.299A pdb=" N SER C 66 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.488A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.488A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.759A pdb=" N GLU F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N MET F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TRP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.759A pdb=" N GLU F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR F 114 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.919A pdb=" N ILE G 34 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.692A pdb=" N TYR G 115 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 9 through 11 removed outlier: 6.512A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 9 through 11 Processing sheet with id=AG4, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AG5, first strand: chain 'K' and resid 27 through 30 removed outlier: 8.057A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU K 224 " --> pdb=" O SER K 205 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 47 through 55 removed outlier: 7.389A pdb=" N THR K 274 " --> pdb=" O ASP K 290 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP K 290 " --> pdb=" O THR K 274 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU K 276 " --> pdb=" O ALA K 288 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA K 288 " --> pdb=" O LEU K 276 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS K 278 " --> pdb=" O THR K 286 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 83 through 85 removed outlier: 3.502A pdb=" N GLY K 103 " --> pdb=" O LEU K 241 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA K 243 " --> pdb=" O ILE K 101 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE K 101 " --> pdb=" O ALA K 243 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ARG K 102 " --> pdb=" O ASN K 121 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL K 126 " --> pdb=" O VAL K 171 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL K 171 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE K 128 " --> pdb=" O GLU K 169 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU K 169 " --> pdb=" O ILE K 128 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL K 130 " --> pdb=" O THR K 167 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU K 132 " --> pdb=" O ASN K 165 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN K 165 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN K 134 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA K 163 " --> pdb=" O GLN K 134 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N CYS K 136 " --> pdb=" O SER K 161 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N SER K 161 " --> pdb=" O CYS K 136 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP K 138 " --> pdb=" O VAL K 159 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL K 159 " --> pdb=" O ASP K 138 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE K 140 " --> pdb=" O PHE K 157 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE K 157 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY K 142 " --> pdb=" O SER K 155 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 83 through 85 removed outlier: 12.799A pdb=" N PHE K 238 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ASN K 137 " --> pdb=" O PHE K 238 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N THR K 240 " --> pdb=" O ASN K 137 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU K 242 " --> pdb=" O PRO K 139 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL K 126 " --> pdb=" O VAL K 171 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL K 171 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE K 128 " --> pdb=" O GLU K 169 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU K 169 " --> pdb=" O ILE K 128 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL K 130 " --> pdb=" O THR K 167 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU K 132 " --> pdb=" O ASN K 165 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN K 165 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN K 134 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA K 163 " --> pdb=" O GLN K 134 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N CYS K 136 " --> pdb=" O SER K 161 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N SER K 161 " --> pdb=" O CYS K 136 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP K 138 " --> pdb=" O VAL K 159 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL K 159 " --> pdb=" O ASP K 138 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE K 140 " --> pdb=" O PHE K 157 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE K 157 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY K 142 " --> pdb=" O SER K 155 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 311 through 319 removed outlier: 5.271A pdb=" N ILE K 312 " --> pdb=" O THR K 599 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR K 599 " --> pdb=" O ILE K 312 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN K 314 " --> pdb=" O VAL K 597 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL K 597 " --> pdb=" O GLN K 314 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY K 594 " --> pdb=" O GLN K 613 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 354 through 358 removed outlier: 3.884A pdb=" N ASN K 394 " --> pdb=" O GLU K 516 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 361 through 362 removed outlier: 6.552A pdb=" N CYS K 361 " --> pdb=" O CYS K 525 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 452 through 454 Processing sheet with id=AH4, first strand: chain 'K' and resid 473 through 474 Processing sheet with id=AH5, first strand: chain 'K' and resid 654 through 655 removed outlier: 6.550A pdb=" N ILE K 670 " --> pdb=" O ILE K 666 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR K1067 " --> pdb=" O HIS K1048 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N HIS K1048 " --> pdb=" O TYR K1067 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE K1095 " --> pdb=" O ALA K1078 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 733 through 736 removed outlier: 4.415A pdb=" N LYS K 733 " --> pdb=" O LEU K 861 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 1120 through 1125 removed outlier: 4.833A pdb=" N ALA K1087 " --> pdb=" O SER K1123 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.544A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.202A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 11.299A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.487A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.487A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AI5, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.760A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N MET M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.760A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR M 114 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AI8, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.919A pdb=" N ILE N 34 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER N 50 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.692A pdb=" N TYR N 115 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'O' and resid 9 through 11 removed outlier: 6.511A pdb=" N TRP O 37 " --> pdb=" O MET O 49 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'O' and resid 9 through 11 Processing sheet with id=AJ3, first strand: chain 'O' and resid 18 through 23 1634 hydrogen bonds defined for protein. 4200 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: 10.89 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9280 1.33 - 1.45: 8169 1.45 - 1.58: 17461 1.58 - 1.71: 1 1.71 - 1.83: 198 Bond restraints: 35109 Sorted by residual: bond pdb=" C5 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.413 1.470 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" C5 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.413 1.469 -0.056 2.00e-02 2.50e+03 7.98e+00 bond pdb=" C5 NAG K1309 " pdb=" O5 NAG K1309 " ideal model delta sigma weight residual 1.413 1.469 -0.056 2.00e-02 2.50e+03 7.94e+00 bond pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.31e+00 bond pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.29e+00 ... (remaining 35104 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 41643 1.63 - 3.26: 5325 3.26 - 4.88: 456 4.88 - 6.51: 399 6.51 - 8.14: 117 Bond angle restraints: 47940 Sorted by residual: angle pdb=" C THR B 791 " pdb=" N PRO B 792 " pdb=" CA PRO B 792 " ideal model delta sigma weight residual 119.66 125.89 -6.23 7.20e-01 1.93e+00 7.48e+01 angle pdb=" C THR K 791 " pdb=" N PRO K 792 " pdb=" CA PRO K 792 " ideal model delta sigma weight residual 119.66 125.86 -6.20 7.20e-01 1.93e+00 7.42e+01 angle pdb=" C THR A 791 " pdb=" N PRO A 792 " pdb=" CA PRO A 792 " ideal model delta sigma weight residual 119.66 125.84 -6.18 7.20e-01 1.93e+00 7.37e+01 angle pdb=" C ASP B1139 " pdb=" N PRO B1140 " pdb=" CA PRO B1140 " ideal model delta sigma weight residual 119.56 127.24 -7.68 1.02e+00 9.61e-01 5.68e+01 angle pdb=" C PRO K 862 " pdb=" N PRO K 863 " pdb=" CA PRO K 863 " ideal model delta sigma weight residual 119.78 127.20 -7.42 1.03e+00 9.43e-01 5.19e+01 ... (remaining 47935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 19281 17.67 - 35.35: 603 35.35 - 53.02: 149 53.02 - 70.70: 49 70.70 - 88.37: 27 Dihedral angle restraints: 20109 sinusoidal: 6963 harmonic: 13146 Sorted by residual: dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual 93.00 53.88 39.12 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 89 " pdb=" CB CYS D 89 " ideal model delta sinusoidal sigma weight residual 93.00 53.90 39.10 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 53.91 39.09 1 1.00e+01 1.00e-02 2.15e+01 ... (remaining 20106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4261 0.070 - 0.140: 1062 0.140 - 0.210: 258 0.210 - 0.280: 41 0.280 - 0.350: 63 Chirality restraints: 5685 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 3.14e+01 chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 3.09e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.96e+01 ... (remaining 5682 not shown) Planarity restraints: 6231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " 0.344 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG T 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " 0.101 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " -0.530 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 1 " 0.344 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG Y 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG Y 1 " 0.101 2.00e-02 2.50e+03 pdb=" N2 NAG Y 1 " -0.530 2.00e-02 2.50e+03 pdb=" O7 NAG Y 1 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " -0.344 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG d 1 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " -0.101 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " 0.530 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.166 2.00e-02 2.50e+03 ... (remaining 6228 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 15361 2.93 - 3.42: 30851 3.42 - 3.91: 59462 3.91 - 4.41: 66934 4.41 - 4.90: 110168 Nonbonded interactions: 282776 Sorted by model distance: nonbonded pdb=" OE2 GLU A 96 " pdb=" NH2 ARG A 190 " model vdw 2.435 3.120 nonbonded pdb=" OE2 GLU K 96 " pdb=" NH2 ARG K 190 " model vdw 2.435 3.120 nonbonded pdb=" OE2 GLU B 96 " pdb=" NH2 ARG B 190 " model vdw 2.435 3.120 nonbonded pdb=" NE2 GLN A 913 " pdb=" O PRO B1090 " model vdw 2.559 3.120 nonbonded pdb=" O PRO A1090 " pdb=" NE2 GLN K 913 " model vdw 2.559 3.120 ... (remaining 282771 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'Z' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'T' selection = chain 'Y' selection = chain 'd' } 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: 4.250 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: 0.060 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 36.020 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.107 35241 Z= 0.620 Angle : 1.239 8.142 48282 Z= 0.827 Chirality : 0.074 0.350 5685 Planarity : 0.009 0.298 6177 Dihedral : 10.784 88.370 11523 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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 are not related in a simple way. whole: 0.49 (0.12), residues: 4497 helix: 0.47 (0.19), residues: 669 sheet: 0.66 (0.14), residues: 1350 loop : 0.21 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 357 TYR 0.041 0.004 TYR L 92 PHE 0.023 0.003 PHE K 898 TRP 0.023 0.005 TRP E 106 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01101 / 0.60 (35109) covalent geometry : angle 1.22428 / 0.83 (47940) SS BOND : bond 0.03549 / 2.72 ( 54) SS BOND : angle 3.09924 / 2.14 ( 108) hydrogen bonds : bond 0.15653 / 10.39 ( 1490) hydrogen bonds : angle 8.44934 / 5.84 ( 4200) link_BETA1-4 : bond 0.05558 / 3.68 ( 18) link_BETA1-4 : angle 2.35863 / 1.64 ( 54) link_BETA1-6 : bond 0.04289 / 2.55 ( 6) link_BETA1-6 : angle 1.95377 / 1.22 ( 18) link_NAG-ASN : bond 0.05429 / 3.72 ( 54) link_NAG-ASN : angle 2.30301 / 1.53 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 696 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 697 MET cc_start: 0.7866 (ptm) cc_final: 0.7582 (ptm) REVERT: E 34 MET cc_start: 0.8208 (tpp) cc_final: 0.7989 (mmm) REVERT: E 48 MET cc_start: 0.7927 (mtp) cc_final: 0.7645 (mtp) REVERT: E 70 MET cc_start: 0.8002 (mtt) cc_final: 0.7448 (mtp) REVERT: C 7 SER cc_start: 0.7162 (t) cc_final: 0.6785 (p) REVERT: F 70 MET cc_start: 0.7964 (mtt) cc_final: 0.7387 (mtp) REVERT: M 70 MET cc_start: 0.8135 (mtt) cc_final: 0.7510 (mtp) outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 0.6856 time to fit residues: 571.6316 Evaluate side-chains 424 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.9980 chunk 424 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 239 GLN A 354 ASN A 394 ASN A 501 ASN A 532 ASN A1101 HIS A1113 GLN D 27 GLN D 38 GLN D 101 GLN E 3 GLN B 207 HIS B 239 GLN B 354 ASN B 564 GLN B 580 GLN B 804 GLN B1113 GLN C 38 GLN F 3 GLN K 30 ASN K 207 HIS K 394 ASN K 532 ASN K 644 GLN K 957 GLN K 969 ASN K1101 HIS L 27 GLN M 3 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.196636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.164471 restraints weight = 36836.356| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.10 r_work: 0.3508 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35241 Z= 0.132 Angle : 0.579 10.200 48282 Z= 0.299 Chirality : 0.044 0.169 5685 Planarity : 0.004 0.033 6177 Dihedral : 4.338 20.632 4860 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.57 % Allowed : 8.48 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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 are not related in a simple way. whole: 1.03 (0.12), residues: 4497 helix: 2.18 (0.20), residues: 642 sheet: 0.84 (0.13), residues: 1362 loop : 0.29 (0.12), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 346 TYR 0.028 0.002 TYR A1138 PHE 0.013 0.002 PHE B 898 TRP 0.011 0.002 TRP E 36 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (35109) covalent geometry : angle 0.56173 / 0.30 (47940) SS BOND : bond 0.00223 / 0.15 ( 54) SS BOND : angle 0.92053 / 0.61 ( 108) hydrogen bonds : bond 0.04702 / 3.16 ( 1490) hydrogen bonds : angle 6.21709 / 4.34 ( 4200) link_BETA1-4 : bond 0.00466 / 0.32 ( 18) link_BETA1-4 : angle 1.46514 / 0.96 ( 54) link_BETA1-6 : bond 0.00586 / 0.35 ( 6) link_BETA1-6 : angle 1.34484 / 0.81 ( 18) link_NAG-ASN : bond 0.00397 / 0.28 ( 54) link_NAG-ASN : angle 2.28601 / 1.44 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 492 time to evaluate : 1.061 Fit side-chains REVERT: A 81 ASN cc_start: 0.7330 (p0) cc_final: 0.7109 (p0) REVERT: A 129 LYS cc_start: 0.7725 (mmtt) cc_final: 0.7519 (mmtt) REVERT: A 239 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: A 314 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: A 354 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.7877 (m110) REVERT: A 394 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7870 (m-40) REVERT: A 498 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7594 (mt0) REVERT: A 619 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7136 (mm-30) REVERT: A 675 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6798 (tm-30) REVERT: A 697 MET cc_start: 0.8489 (ptm) cc_final: 0.8169 (ptm) REVERT: A 796 ASP cc_start: 0.7639 (t70) cc_final: 0.7217 (p0) REVERT: A 988 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6388 (mm-30) REVERT: A 1058 HIS cc_start: 0.8511 (m170) cc_final: 0.8278 (m-70) REVERT: D 55 ARG cc_start: 0.8020 (ttm110) cc_final: 0.7725 (ttm-80) REVERT: D 64 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.8040 (m) REVERT: E 34 MET cc_start: 0.8838 (tpp) cc_final: 0.8571 (mmm) REVERT: E 48 MET cc_start: 0.8776 (mtp) cc_final: 0.8393 (mtp) REVERT: E 70 MET cc_start: 0.8061 (mtt) cc_final: 0.7651 (mtt) REVERT: B 298 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: B 307 THR cc_start: 0.8661 (t) cc_final: 0.8196 (m) REVERT: B 314 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: B 324 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: B 354 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8134 (m110) REVERT: B 357 ARG cc_start: 0.8333 (ttt180) cc_final: 0.8128 (ttt180) REVERT: B 583 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6965 (tp30) REVERT: B 987 PRO cc_start: 0.7867 (Cg_exo) cc_final: 0.7466 (Cg_endo) REVERT: B 988 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6048 (mm-30) REVERT: C 4 MET cc_start: 0.7024 (mmp) cc_final: 0.6656 (mmp) REVERT: C 27 GLN cc_start: 0.7377 (pt0) cc_final: 0.7175 (pt0) REVERT: C 55 ARG cc_start: 0.8096 (ttm110) cc_final: 0.7812 (ttm110) REVERT: F 48 MET cc_start: 0.8831 (mtp) cc_final: 0.8584 (mtp) REVERT: F 81 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7538 (ttp) REVERT: K 207 HIS cc_start: 0.7383 (t-90) cc_final: 0.6701 (m90) REVERT: K 314 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: K 386 LYS cc_start: 0.8931 (mttt) cc_final: 0.8696 (mtmm) REVERT: K 528 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8166 (ttmt) REVERT: K 702 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6623 (tt0) REVERT: K 900 MET cc_start: 0.8596 (ttm) cc_final: 0.8345 (ttm) REVERT: K 957 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: K 988 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6227 (mm-30) REVERT: K 1019 ARG cc_start: 0.8751 (ttp-110) cc_final: 0.8526 (ttm110) REVERT: K 1138 TYR cc_start: 0.7838 (t80) cc_final: 0.7516 (t80) REVERT: M 48 MET cc_start: 0.8749 (mtp) cc_final: 0.8304 (mtp) REVERT: M 70 MET cc_start: 0.8083 (mtt) cc_final: 0.7665 (mtt) outliers start: 84 outliers final: 25 residues processed: 539 average time/residue: 0.6402 time to fit residues: 416.3637 Evaluate side-chains 461 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 416 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 314 GLN Chi-restraints excluded: chain K residue 528 LYS Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 702 GLU Chi-restraints excluded: chain K residue 731 MET Chi-restraints excluded: chain K residue 957 GLN Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 221 optimal weight: 1.9990 chunk 382 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 350 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 chunk 427 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 409 optimal weight: 2.9990 chunk 379 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 354 ASN A 394 ASN A 532 ASN A 804 GLN A 901 GLN A1101 HIS D 27 GLN D 91 GLN D 101 GLN B 81 ASN B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** K 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 394 ASN K 532 ASN K 580 GLN K 644 GLN K 804 GLN K 901 GLN K 957 GLN ** K1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1113 GLN L 27 GLN M 3 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.192299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.159778 restraints weight = 36174.647| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.08 r_work: 0.3419 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 35241 Z= 0.258 Angle : 0.662 9.358 48282 Z= 0.342 Chirality : 0.048 0.217 5685 Planarity : 0.005 0.065 6177 Dihedral : 4.729 23.424 4860 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.89 % Allowed : 9.92 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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 are not related in a simple way. whole: 0.86 (0.12), residues: 4497 helix: 2.14 (0.20), residues: 624 sheet: 0.76 (0.13), residues: 1362 loop : 0.14 (0.12), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1039 TYR 0.031 0.002 TYR L 92 PHE 0.027 0.003 PHE B 898 TRP 0.019 0.003 TRP M 36 HIS 0.008 0.002 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.26 (35109) covalent geometry : angle 0.64403 / 0.34 (47940) SS BOND : bond 0.00444 / 0.31 ( 54) SS BOND : angle 1.20114 / 0.80 ( 108) hydrogen bonds : bond 0.05280 / 3.54 ( 1490) hydrogen bonds : angle 6.13992 / 4.28 ( 4200) link_BETA1-4 : bond 0.00496 / 0.34 ( 18) link_BETA1-4 : angle 1.27867 / 0.88 ( 54) link_BETA1-6 : bond 0.00353 / 0.21 ( 6) link_BETA1-6 : angle 1.38689 / 0.85 ( 18) link_NAG-ASN : bond 0.00409 / 0.29 ( 54) link_NAG-ASN : angle 2.49618 / 1.59 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 432 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: A 619 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7084 (mm-30) REVERT: A 675 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: A 697 MET cc_start: 0.8511 (ptm) cc_final: 0.8199 (ptm) REVERT: A 702 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: A 731 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8086 (mtp) REVERT: A 740 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8489 (ttt) REVERT: E 38 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7590 (ttm170) REVERT: E 48 MET cc_start: 0.8860 (mtp) cc_final: 0.8486 (mtp) REVERT: B 224 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: B 314 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: B 324 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: B 574 ASP cc_start: 0.8004 (p0) cc_final: 0.7542 (t0) REVERT: B 787 GLN cc_start: 0.8562 (mp10) cc_final: 0.8326 (mm-40) REVERT: B 988 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6238 (mm-30) REVERT: B 1073 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8218 (ptmt) REVERT: B 1091 ARG cc_start: 0.7987 (mtt90) cc_final: 0.7737 (mtt-85) REVERT: C 4 MET cc_start: 0.7082 (mmp) cc_final: 0.6762 (mmp) REVERT: C 64 SER cc_start: 0.8168 (OUTLIER) cc_final: 0.7907 (m) REVERT: F 81 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7801 (ttp) REVERT: K 81 ASN cc_start: 0.7548 (p0) cc_final: 0.7328 (p0) REVERT: K 207 HIS cc_start: 0.7234 (t-90) cc_final: 0.6607 (m90) REVERT: K 224 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: K 427 ASP cc_start: 0.8025 (m-30) cc_final: 0.7722 (t0) REVERT: K 616 ASN cc_start: 0.7545 (t0) cc_final: 0.7108 (t0) REVERT: K 619 GLU cc_start: 0.7622 (mp0) cc_final: 0.6900 (mp0) REVERT: K 702 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6693 (tt0) REVERT: K 1019 ARG cc_start: 0.8734 (ttp-110) cc_final: 0.8493 (ttm110) REVERT: K 1138 TYR cc_start: 0.7841 (t80) cc_final: 0.7548 (t80) REVERT: L 34 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8392 (tm) REVERT: L 64 SER cc_start: 0.8198 (OUTLIER) cc_final: 0.7932 (m) REVERT: M 48 MET cc_start: 0.8878 (mtp) cc_final: 0.8434 (mtp) REVERT: M 67 ARG cc_start: 0.7536 (mtp180) cc_final: 0.7293 (ttp80) REVERT: M 70 MET cc_start: 0.7955 (mtt) cc_final: 0.7710 (mtt) outliers start: 127 outliers final: 56 residues processed: 499 average time/residue: 0.6464 time to fit residues: 387.7832 Evaluate side-chains 473 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 400 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 224 GLU Chi-restraints excluded: chain K residue 359 SER Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 591 SER Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 702 GLU Chi-restraints excluded: chain K residue 731 MET Chi-restraints excluded: chain K residue 754 LEU Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 1073 LYS Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 63 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 22 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 370 optimal weight: 0.5980 chunk 443 optimal weight: 30.0000 chunk 166 optimal weight: 0.9980 chunk 444 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 396 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 957 GLN A1101 HIS D 91 GLN D 101 GLN E 3 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 394 ASN B 564 GLN B 957 GLN C 27 GLN F 3 GLN K 394 ASN K 532 ASN K 613 GLN K 957 GLN K1101 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.193578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.162149 restraints weight = 36232.211| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.04 r_work: 0.3437 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.005 0.062 35241 Z= 0.199 Angle : 0.596 8.248 48282 Z= 0.307 Chirality : 0.046 0.236 5685 Planarity : 0.004 0.045 6177 Dihedral : 4.591 24.539 4860 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.61 % Allowed : 10.93 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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 are not related in a simple way. whole: 0.81 (0.12), residues: 4497 helix: 2.26 (0.20), residues: 624 sheet: 0.66 (0.13), residues: 1428 loop : 0.09 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.028 0.002 TYR L 92 PHE 0.025 0.002 PHE B 898 TRP 0.015 0.002 TRP E 106 HIS 0.006 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (35109) covalent geometry : angle 0.58105 / 0.30 (47940) SS BOND : bond 0.00334 / 0.23 ( 54) SS BOND : angle 0.97656 / 0.64 ( 108) hydrogen bonds : bond 0.04760 / 3.20 ( 1490) hydrogen bonds : angle 5.91031 / 4.12 ( 4200) link_BETA1-4 : bond 0.00522 / 0.35 ( 18) link_BETA1-4 : angle 1.14100 / 0.76 ( 54) link_BETA1-6 : bond 0.00265 / 0.16 ( 6) link_BETA1-6 : angle 1.37072 / 0.85 ( 18) link_NAG-ASN : bond 0.00280 / 0.19 ( 54) link_NAG-ASN : angle 2.13548 / 1.35 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 429 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7574 (tptt) REVERT: A 314 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: A 346 ARG cc_start: 0.7562 (mmm160) cc_final: 0.7324 (mmm160) REVERT: A 428 ASP cc_start: 0.8287 (p0) cc_final: 0.8044 (p0) REVERT: A 619 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6896 (mm-30) REVERT: A 675 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.7159 (tm-30) REVERT: A 697 MET cc_start: 0.8505 (ptm) cc_final: 0.8188 (ptm) REVERT: A 740 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8556 (ttt) REVERT: A 747 THR cc_start: 0.8729 (m) cc_final: 0.8307 (p) REVERT: E 34 MET cc_start: 0.8727 (tpp) cc_final: 0.8525 (mmm) REVERT: E 38 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7691 (ttm170) REVERT: E 43 GLN cc_start: 0.7412 (tp40) cc_final: 0.7039 (mt0) REVERT: E 48 MET cc_start: 0.8810 (mtp) cc_final: 0.8404 (mtp) REVERT: B 224 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: B 307 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8380 (m) REVERT: B 324 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7402 (tt0) REVERT: B 574 ASP cc_start: 0.7917 (p0) cc_final: 0.7629 (t0) REVERT: B 787 GLN cc_start: 0.8447 (mp10) cc_final: 0.8246 (mm-40) REVERT: B 814 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7756 (mmtm) REVERT: B 935 GLN cc_start: 0.7556 (tp40) cc_final: 0.7317 (tt0) REVERT: B 988 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6246 (mm-30) REVERT: B 1073 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8091 (ptmt) REVERT: B 1091 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7746 (mtt-85) REVERT: C 64 SER cc_start: 0.8073 (OUTLIER) cc_final: 0.7855 (m) REVERT: F 81 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7928 (ttp) REVERT: K 81 ASN cc_start: 0.7528 (p0) cc_final: 0.7302 (p0) REVERT: K 207 HIS cc_start: 0.7196 (t-90) cc_final: 0.6604 (m90) REVERT: K 224 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: K 346 ARG cc_start: 0.7375 (mmm-85) cc_final: 0.7152 (mmm160) REVERT: K 427 ASP cc_start: 0.8043 (m-30) cc_final: 0.7829 (m-30) REVERT: K 644 GLN cc_start: 0.8730 (tp40) cc_final: 0.8472 (tp-100) REVERT: K 988 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6322 (mm-30) REVERT: K 1138 TYR cc_start: 0.7897 (t80) cc_final: 0.7634 (t80) REVERT: L 34 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8384 (tm) REVERT: M 48 MET cc_start: 0.8838 (mtp) cc_final: 0.8341 (mtp) REVERT: M 70 MET cc_start: 0.7940 (mtt) cc_final: 0.7480 (mtt) outliers start: 118 outliers final: 53 residues processed: 495 average time/residue: 0.6331 time to fit residues: 377.0194 Evaluate side-chains 464 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 396 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 224 GLU Chi-restraints excluded: chain K residue 359 SER Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 63 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 40 optimal weight: 0.7980 chunk 364 optimal weight: 3.9990 chunk 218 optimal weight: 0.0970 chunk 155 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 400 optimal weight: 0.9990 chunk 0 optimal weight: 10.9990 chunk 304 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 394 ASN A 779 GLN A 957 GLN A1101 HIS D 91 GLN D 101 GLN E 3 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 613 GLN B 957 GLN F 3 GLN K 394 ASN K 957 GLN K1101 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.193560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.159734 restraints weight = 36502.218| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.10 r_work: 0.3420 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 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 0.041 35241 Z= 0.138 Angle : 0.542 7.395 48282 Z= 0.278 Chirality : 0.044 0.307 5685 Planarity : 0.004 0.040 6177 Dihedral : 4.319 22.903 4860 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.49 % Allowed : 11.36 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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 are not related in a simple way. whole: 0.90 (0.12), residues: 4497 helix: 2.51 (0.20), residues: 627 sheet: 0.71 (0.13), residues: 1392 loop : 0.11 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 346 TYR 0.020 0.001 TYR C 92 PHE 0.020 0.001 PHE B 898 TRP 0.016 0.001 TRP E 106 HIS 0.005 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (35109) covalent geometry : angle 0.52832 / 0.28 (47940) SS BOND : bond 0.00262 / 0.18 ( 54) SS BOND : angle 0.83832 / 0.54 ( 108) hydrogen bonds : bond 0.04207 / 2.82 ( 1490) hydrogen bonds : angle 5.64683 / 3.94 ( 4200) link_BETA1-4 : bond 0.00550 / 0.37 ( 18) link_BETA1-4 : angle 1.10096 / 0.73 ( 54) link_BETA1-6 : bond 0.00287 / 0.17 ( 6) link_BETA1-6 : angle 1.30333 / 0.82 ( 18) link_NAG-ASN : bond 0.00282 / 0.18 ( 54) link_NAG-ASN : angle 2.00487 / 1.27 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 428 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7636 (tptt) REVERT: A 307 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8550 (m) REVERT: A 346 ARG cc_start: 0.7658 (mmm160) cc_final: 0.7418 (mmm160) REVERT: A 697 MET cc_start: 0.8474 (ptm) cc_final: 0.8162 (ptm) REVERT: A 702 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7250 (tt0) REVERT: A 740 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8491 (ttt) REVERT: A 747 THR cc_start: 0.8703 (m) cc_final: 0.8289 (p) REVERT: D 75 THR cc_start: 0.7930 (m) cc_final: 0.7622 (t) REVERT: E 34 MET cc_start: 0.8697 (tpp) cc_final: 0.8464 (mmm) REVERT: E 43 GLN cc_start: 0.7439 (tp40) cc_final: 0.7087 (mt0) REVERT: E 48 MET cc_start: 0.8881 (mtp) cc_final: 0.8515 (mtp) REVERT: B 190 ARG cc_start: 0.7475 (mtp85) cc_final: 0.7257 (mtt-85) REVERT: B 207 HIS cc_start: 0.7671 (t70) cc_final: 0.7098 (m-70) REVERT: B 307 THR cc_start: 0.8767 (t) cc_final: 0.8384 (m) REVERT: B 324 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: B 574 ASP cc_start: 0.7833 (p0) cc_final: 0.7470 (OUTLIER) REVERT: B 814 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7779 (mmtm) REVERT: B 933 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8256 (mtpp) REVERT: B 935 GLN cc_start: 0.7632 (tp40) cc_final: 0.7343 (tt0) REVERT: B 1073 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8063 (ptmt) REVERT: B 1091 ARG cc_start: 0.8017 (mtt90) cc_final: 0.7752 (mtt-85) REVERT: F 82 GLU cc_start: 0.7834 (tp30) cc_final: 0.7609 (mm-30) REVERT: K 81 ASN cc_start: 0.7491 (p0) cc_final: 0.7249 (p0) REVERT: K 207 HIS cc_start: 0.7250 (t-90) cc_final: 0.6689 (m90) REVERT: K 616 ASN cc_start: 0.7541 (t0) cc_final: 0.7012 (t0) REVERT: K 619 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: K 644 GLN cc_start: 0.8754 (tp40) cc_final: 0.8509 (tp-100) REVERT: K 1138 TYR cc_start: 0.7933 (t80) cc_final: 0.7635 (t80) REVERT: L 34 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8389 (tm) REVERT: M 48 MET cc_start: 0.8828 (mtp) cc_final: 0.8394 (mtp) REVERT: M 70 MET cc_start: 0.8000 (mtt) cc_final: 0.7602 (mtt) outliers start: 114 outliers final: 49 residues processed: 488 average time/residue: 0.6617 time to fit residues: 390.7446 Evaluate side-chains 464 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 407 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 619 GLU Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain K residue 1073 LYS Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 63 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 363 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 399 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 275 optimal weight: 4.9990 chunk 293 optimal weight: 0.8980 chunk 403 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 394 ASN A 613 GLN A 957 GLN A1101 HIS D 91 GLN D 101 GLN E 3 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 564 GLN B 957 GLN F 3 GLN K 394 ASN K 957 GLN ** K1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.193052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.159213 restraints weight = 36328.480| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.10 r_work: 0.3411 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35241 Z= 0.157 Angle : 0.560 13.628 48282 Z= 0.286 Chirality : 0.046 0.910 5685 Planarity : 0.004 0.053 6177 Dihedral : 4.346 23.170 4860 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.58 % Allowed : 11.94 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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 are not related in a simple way. whole: 0.87 (0.12), residues: 4497 helix: 2.51 (0.20), residues: 624 sheet: 0.68 (0.13), residues: 1437 loop : 0.08 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 346 TYR 0.024 0.002 TYR L 92 PHE 0.022 0.002 PHE B 898 TRP 0.015 0.002 TRP E 106 HIS 0.005 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (35109) covalent geometry : angle 0.54490 / 0.28 (47940) SS BOND : bond 0.00280 / 0.20 ( 54) SS BOND : angle 0.85965 / 0.55 ( 108) hydrogen bonds : bond 0.04312 / 2.89 ( 1490) hydrogen bonds : angle 5.61087 / 3.91 ( 4200) link_BETA1-4 : bond 0.00503 / 0.34 ( 18) link_BETA1-4 : angle 1.11220 / 0.74 ( 54) link_BETA1-6 : bond 0.00267 / 0.16 ( 6) link_BETA1-6 : angle 1.33581 / 0.83 ( 18) link_NAG-ASN : bond 0.00495 / 0.22 ( 54) link_NAG-ASN : angle 2.15107 / 1.36 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 407 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7655 (tptt) REVERT: A 307 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8562 (m) REVERT: A 346 ARG cc_start: 0.7645 (mmm160) cc_final: 0.7406 (mmm160) REVERT: A 498 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7581 (mt0) REVERT: A 675 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: A 697 MET cc_start: 0.8503 (ptm) cc_final: 0.8198 (ptm) REVERT: A 702 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: A 747 THR cc_start: 0.8704 (m) cc_final: 0.8279 (p) REVERT: D 75 THR cc_start: 0.7916 (m) cc_final: 0.7618 (t) REVERT: E 48 MET cc_start: 0.8914 (mtp) cc_final: 0.8540 (mtp) REVERT: E 90 ASP cc_start: 0.7627 (m-30) cc_final: 0.7388 (m-30) REVERT: B 224 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: B 307 THR cc_start: 0.8764 (t) cc_final: 0.8375 (m) REVERT: B 324 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: B 427 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: B 702 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: B 814 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7760 (mmtm) REVERT: B 935 GLN cc_start: 0.7620 (tp40) cc_final: 0.7387 (tt0) REVERT: B 1091 ARG cc_start: 0.8031 (mtt90) cc_final: 0.7756 (mtt-85) REVERT: F 82 GLU cc_start: 0.7790 (tp30) cc_final: 0.7561 (mm-30) REVERT: K 81 ASN cc_start: 0.7358 (p0) cc_final: 0.7129 (p0) REVERT: K 207 HIS cc_start: 0.7230 (t-90) cc_final: 0.6695 (m90) REVERT: K 224 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: K 346 ARG cc_start: 0.7812 (mmm160) cc_final: 0.7552 (mmm-85) REVERT: K 528 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8226 (ttpp) REVERT: K 616 ASN cc_start: 0.7691 (t0) cc_final: 0.7268 (t0) REVERT: K 619 GLU cc_start: 0.7622 (mp0) cc_final: 0.7059 (mp0) REVERT: K 644 GLN cc_start: 0.8777 (tp40) cc_final: 0.8493 (tp-100) REVERT: K 740 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8447 (ttt) REVERT: K 1138 TYR cc_start: 0.7958 (t80) cc_final: 0.7701 (t80) REVERT: L 34 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8399 (tm) REVERT: M 48 MET cc_start: 0.8854 (mtp) cc_final: 0.8445 (mtp) REVERT: M 70 MET cc_start: 0.7936 (mtt) cc_final: 0.7542 (mtt) outliers start: 117 outliers final: 62 residues processed: 477 average time/residue: 0.6744 time to fit residues: 389.0431 Evaluate side-chains 475 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 400 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 224 GLU Chi-restraints excluded: chain K residue 359 SER Chi-restraints excluded: chain K residue 427 ASP Chi-restraints excluded: chain K residue 528 LYS Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 586 ASP Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 740 MET Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 1073 LYS Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 63 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 394 optimal weight: 0.8980 chunk 416 optimal weight: 3.9990 chunk 378 optimal weight: 1.9990 chunk 284 optimal weight: 20.0000 chunk 233 optimal weight: 0.9990 chunk 224 optimal weight: 0.0770 chunk 300 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 443 optimal weight: 8.9990 chunk 146 optimal weight: 50.0000 chunk 240 optimal weight: 0.8980 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 394 ASN A 957 GLN A1101 HIS D 91 GLN D 101 GLN E 3 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN F 3 GLN K 394 ASN K 957 GLN ** K1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.193020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.159364 restraints weight = 36515.936| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.09 r_work: 0.3414 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35241 Z= 0.160 Angle : 0.561 11.565 48282 Z= 0.287 Chirality : 0.045 0.600 5685 Planarity : 0.004 0.039 6177 Dihedral : 4.338 22.947 4860 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.67 % Allowed : 12.12 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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 are not related in a simple way. whole: 0.83 (0.12), residues: 4497 helix: 2.29 (0.20), residues: 645 sheet: 0.70 (0.13), residues: 1452 loop : 0.05 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 346 TYR 0.024 0.002 TYR L 92 PHE 0.023 0.002 PHE B 898 TRP 0.014 0.002 TRP E 106 HIS 0.005 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (35109) covalent geometry : angle 0.54613 / 0.28 (47940) SS BOND : bond 0.00288 / 0.20 ( 54) SS BOND : angle 0.85747 / 0.55 ( 108) hydrogen bonds : bond 0.04303 / 2.89 ( 1490) hydrogen bonds : angle 5.58146 / 3.89 ( 4200) link_BETA1-4 : bond 0.00489 / 0.33 ( 18) link_BETA1-4 : angle 1.12449 / 0.75 ( 54) link_BETA1-6 : bond 0.00250 / 0.15 ( 6) link_BETA1-6 : angle 1.34298 / 0.83 ( 18) link_NAG-ASN : bond 0.00526 / 0.23 ( 54) link_NAG-ASN : angle 2.11703 / 1.35 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 412 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7934 (mmtt) cc_final: 0.7643 (tptp) REVERT: A 307 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8559 (m) REVERT: A 697 MET cc_start: 0.8489 (ptm) cc_final: 0.8146 (ptm) REVERT: A 702 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: A 747 THR cc_start: 0.8656 (m) cc_final: 0.8246 (p) REVERT: D 4 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6767 (mmp) REVERT: D 34 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8608 (tm) REVERT: D 75 THR cc_start: 0.7916 (m) cc_final: 0.7619 (t) REVERT: E 43 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6958 (mt0) REVERT: E 48 MET cc_start: 0.8907 (mtp) cc_final: 0.8532 (mtp) REVERT: B 207 HIS cc_start: 0.7586 (t70) cc_final: 0.7047 (m90) REVERT: B 224 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: B 307 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8366 (m) REVERT: B 324 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: B 427 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7640 (m-30) REVERT: B 498 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: B 814 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7710 (mmtm) REVERT: B 933 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8285 (mtpp) REVERT: B 935 GLN cc_start: 0.7629 (tp40) cc_final: 0.7427 (tt0) REVERT: B 1091 ARG cc_start: 0.8044 (mtt90) cc_final: 0.7763 (mtt-85) REVERT: C 4 MET cc_start: 0.6804 (mmm) cc_final: 0.6519 (mmp) REVERT: C 24 ARG cc_start: 0.7623 (ttp-110) cc_final: 0.6930 (mmp-170) REVERT: F 82 GLU cc_start: 0.7758 (tp30) cc_final: 0.7495 (mm-30) REVERT: K 81 ASN cc_start: 0.7358 (p0) cc_final: 0.7130 (p0) REVERT: K 207 HIS cc_start: 0.7232 (t-90) cc_final: 0.6682 (m90) REVERT: K 224 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7900 (mt-10) REVERT: K 346 ARG cc_start: 0.7856 (mmm160) cc_final: 0.7525 (mmm-85) REVERT: K 616 ASN cc_start: 0.7622 (t0) cc_final: 0.7239 (t0) REVERT: K 619 GLU cc_start: 0.7613 (mp0) cc_final: 0.7090 (mp0) REVERT: K 644 GLN cc_start: 0.8750 (tp40) cc_final: 0.8474 (tp-100) REVERT: K 957 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: K 1138 TYR cc_start: 0.7879 (t80) cc_final: 0.7658 (t80) REVERT: L 34 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8389 (tm) REVERT: M 48 MET cc_start: 0.8854 (mtp) cc_final: 0.8413 (mtp) REVERT: M 70 MET cc_start: 0.8031 (mtt) cc_final: 0.7599 (mtt) outliers start: 120 outliers final: 63 residues processed: 482 average time/residue: 0.6886 time to fit residues: 401.7381 Evaluate side-chains 479 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 401 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 224 GLU Chi-restraints excluded: chain K residue 359 SER Chi-restraints excluded: chain K residue 427 ASP Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 586 ASP Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 772 VAL Chi-restraints excluded: chain K residue 957 GLN Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 1073 LYS Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 63 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 378 optimal weight: 0.7980 chunk 136 optimal weight: 30.0000 chunk 241 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 chunk 186 optimal weight: 0.5980 chunk 432 optimal weight: 30.0000 chunk 411 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 385 optimal weight: 2.9990 chunk 446 optimal weight: 50.0000 chunk 308 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 394 ASN A 957 GLN A1101 HIS D 91 GLN D 101 GLN B 121 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 957 GLN F 3 GLN K 394 ASN K 957 GLN K1101 HIS M 3 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.193743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.160134 restraints weight = 36570.787| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.09 r_work: 0.3427 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35241 Z= 0.133 Angle : 0.541 14.006 48282 Z= 0.277 Chirality : 0.044 0.596 5685 Planarity : 0.004 0.038 6177 Dihedral : 4.223 22.057 4860 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.24 % Allowed : 12.79 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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 are not related in a simple way. whole: 0.88 (0.12), residues: 4497 helix: 2.31 (0.20), residues: 651 sheet: 0.71 (0.13), residues: 1425 loop : 0.10 (0.13), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 346 TYR 0.023 0.001 TYR A1138 PHE 0.020 0.001 PHE B 898 TRP 0.014 0.001 TRP E 106 HIS 0.004 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (35109) covalent geometry : angle 0.52591 / 0.27 (47940) SS BOND : bond 0.00228 / 0.16 ( 54) SS BOND : angle 0.78306 / 0.51 ( 108) hydrogen bonds : bond 0.04053 / 2.72 ( 1490) hydrogen bonds : angle 5.47426 / 3.82 ( 4200) link_BETA1-4 : bond 0.00497 / 0.33 ( 18) link_BETA1-4 : angle 1.10651 / 0.74 ( 54) link_BETA1-6 : bond 0.00292 / 0.17 ( 6) link_BETA1-6 : angle 1.32215 / 0.82 ( 18) link_NAG-ASN : bond 0.00740 / 0.27 ( 54) link_NAG-ASN : angle 2.11039 / 1.34 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 412 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7290 (mp) REVERT: A 129 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7683 (tptp) REVERT: A 307 THR cc_start: 0.8845 (t) cc_final: 0.8564 (m) REVERT: A 697 MET cc_start: 0.8486 (ptm) cc_final: 0.8182 (ptm) REVERT: A 702 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: A 740 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8532 (ttt) REVERT: A 747 THR cc_start: 0.8633 (m) cc_final: 0.8275 (p) REVERT: D 34 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8652 (tm) REVERT: D 75 THR cc_start: 0.7906 (m) cc_final: 0.7619 (t) REVERT: E 43 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7003 (mt0) REVERT: E 48 MET cc_start: 0.8888 (mtp) cc_final: 0.8516 (mtp) REVERT: B 207 HIS cc_start: 0.7612 (t70) cc_final: 0.7069 (m90) REVERT: B 307 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8351 (m) REVERT: B 324 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: B 346 ARG cc_start: 0.7582 (mmm160) cc_final: 0.7302 (mmm160) REVERT: B 427 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: B 498 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: B 814 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7770 (mmtm) REVERT: C 4 MET cc_start: 0.6563 (mmm) cc_final: 0.6242 (mmp) REVERT: C 24 ARG cc_start: 0.7586 (ttp-110) cc_final: 0.7030 (mmp-170) REVERT: F 82 GLU cc_start: 0.7815 (tp30) cc_final: 0.7546 (mm-30) REVERT: K 81 ASN cc_start: 0.7352 (p0) cc_final: 0.7124 (p0) REVERT: K 207 HIS cc_start: 0.7280 (t-90) cc_final: 0.6739 (m90) REVERT: K 224 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: K 346 ARG cc_start: 0.7875 (mmm160) cc_final: 0.7567 (mmm-85) REVERT: K 498 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7699 (mt0) REVERT: K 616 ASN cc_start: 0.7579 (t0) cc_final: 0.7244 (t0) REVERT: K 619 GLU cc_start: 0.7632 (mp0) cc_final: 0.7152 (mp0) REVERT: K 644 GLN cc_start: 0.8775 (tp40) cc_final: 0.8483 (tp-100) REVERT: K 1138 TYR cc_start: 0.7950 (t80) cc_final: 0.7745 (t80) REVERT: L 34 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8402 (tm) REVERT: M 43 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7341 (mt0) REVERT: M 48 MET cc_start: 0.8809 (mtp) cc_final: 0.8427 (mtp) REVERT: M 70 MET cc_start: 0.7991 (mtt) cc_final: 0.7539 (mtt) outliers start: 106 outliers final: 60 residues processed: 476 average time/residue: 0.6641 time to fit residues: 384.2729 Evaluate side-chains 466 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 392 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 224 GLU Chi-restraints excluded: chain K residue 359 SER Chi-restraints excluded: chain K residue 427 ASP Chi-restraints excluded: chain K residue 498 GLN Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 586 ASP Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 772 VAL Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 1073 LYS Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 63 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 18 optimal weight: 3.9990 chunk 438 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 301 optimal weight: 0.6980 chunk 420 optimal weight: 1.9990 chunk 428 optimal weight: 40.0000 chunk 6 optimal weight: 0.7980 chunk 321 optimal weight: 2.9990 chunk 355 optimal weight: 0.6980 chunk 303 optimal weight: 2.9990 chunk 362 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 394 ASN A 613 GLN A 957 GLN A1101 HIS D 91 GLN D 101 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN F 3 GLN K 245 HIS K 394 ASN K 957 GLN ** K1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.192422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.158589 restraints weight = 36360.114| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.10 r_work: 0.3403 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 35241 Z= 0.190 Angle : 0.596 17.527 48282 Z= 0.303 Chirality : 0.047 0.843 5685 Planarity : 0.004 0.039 6177 Dihedral : 4.416 23.636 4860 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.09 % Allowed : 13.19 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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 are not related in a simple way. whole: 0.82 (0.12), residues: 4497 helix: 2.21 (0.20), residues: 645 sheet: 0.73 (0.13), residues: 1455 loop : 0.04 (0.13), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 346 TYR 0.029 0.002 TYR L 92 PHE 0.025 0.002 PHE B 898 TRP 0.013 0.002 TRP E 106 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (35109) covalent geometry : angle 0.57621 / 0.30 (47940) SS BOND : bond 0.00345 / 0.24 ( 54) SS BOND : angle 0.90662 / 0.59 ( 108) hydrogen bonds : bond 0.04492 / 3.01 ( 1490) hydrogen bonds : angle 5.59266 / 3.90 ( 4200) link_BETA1-4 : bond 0.00472 / 0.31 ( 18) link_BETA1-4 : angle 1.15702 / 0.77 ( 54) link_BETA1-6 : bond 0.00232 / 0.14 ( 6) link_BETA1-6 : angle 1.38962 / 0.85 ( 18) link_NAG-ASN : bond 0.00696 / 0.39 ( 54) link_NAG-ASN : angle 2.54760 / 1.46 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 400 time to evaluate : 1.270 Fit side-chains REVERT: A 129 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7641 (tptp) REVERT: A 307 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8560 (m) REVERT: A 697 MET cc_start: 0.8501 (ptm) cc_final: 0.8199 (ptm) REVERT: A 702 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7368 (tt0) REVERT: A 747 THR cc_start: 0.8684 (m) cc_final: 0.8293 (p) REVERT: D 75 THR cc_start: 0.7897 (m) cc_final: 0.7602 (t) REVERT: E 48 MET cc_start: 0.8909 (mtp) cc_final: 0.8523 (mtp) REVERT: B 207 HIS cc_start: 0.7555 (t70) cc_final: 0.7073 (m90) REVERT: B 307 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8350 (m) REVERT: B 324 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: B 498 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7920 (mt0) REVERT: B 814 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7733 (mmtm) REVERT: B 1091 ARG cc_start: 0.8036 (mtt90) cc_final: 0.7740 (mtt-85) REVERT: C 24 ARG cc_start: 0.7631 (ttp-110) cc_final: 0.7015 (mmp-170) REVERT: F 82 GLU cc_start: 0.7783 (tp30) cc_final: 0.7565 (mm-30) REVERT: K 81 ASN cc_start: 0.7354 (p0) cc_final: 0.7150 (p0) REVERT: K 207 HIS cc_start: 0.7276 (t-90) cc_final: 0.6724 (m90) REVERT: K 224 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: K 287 ASP cc_start: 0.7987 (t0) cc_final: 0.7503 (t70) REVERT: K 346 ARG cc_start: 0.7904 (mmm160) cc_final: 0.7511 (mmm-85) REVERT: K 528 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8309 (ttpp) REVERT: K 616 ASN cc_start: 0.7622 (t0) cc_final: 0.7288 (t0) REVERT: K 619 GLU cc_start: 0.7640 (mp0) cc_final: 0.7113 (mp0) REVERT: K 644 GLN cc_start: 0.8778 (tp40) cc_final: 0.8480 (tp-100) REVERT: K 1138 TYR cc_start: 0.7931 (t80) cc_final: 0.7708 (t80) REVERT: L 34 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8393 (tm) REVERT: M 48 MET cc_start: 0.8860 (mtp) cc_final: 0.8497 (mtp) REVERT: M 70 MET cc_start: 0.8036 (mtt) cc_final: 0.7602 (mtt) outliers start: 101 outliers final: 65 residues processed: 461 average time/residue: 0.6076 time to fit residues: 340.9103 Evaluate side-chains 469 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 395 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 224 GLU Chi-restraints excluded: chain K residue 359 SER Chi-restraints excluded: chain K residue 427 ASP Chi-restraints excluded: chain K residue 528 LYS Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 586 ASP Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 772 VAL Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 1001 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 428 optimal weight: 50.0000 chunk 67 optimal weight: 0.9990 chunk 320 optimal weight: 0.0010 chunk 256 optimal weight: 7.9990 chunk 423 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 299 optimal weight: 20.0000 chunk 70 optimal weight: 0.3980 chunk 351 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 394 ASN A 779 GLN A 804 GLN A 935 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN B 121 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 957 GLN F 3 GLN K 394 ASN K 957 GLN ** K1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.194054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.160429 restraints weight = 36425.079| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.09 r_work: 0.3438 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35241 Z= 0.123 Angle : 0.535 11.227 48282 Z= 0.273 Chirality : 0.045 0.603 5685 Planarity : 0.004 0.038 6177 Dihedral : 4.195 22.652 4860 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.54 % Allowed : 13.90 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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 are not related in a simple way. whole: 0.89 (0.12), residues: 4497 helix: 2.36 (0.20), residues: 651 sheet: 0.73 (0.13), residues: 1425 loop : 0.09 (0.13), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 346 TYR 0.024 0.001 TYR A1138 PHE 0.020 0.001 PHE B 898 TRP 0.014 0.001 TRP E 106 HIS 0.004 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (35109) covalent geometry : angle 0.51817 / 0.27 (47940) SS BOND : bond 0.00205 / 0.15 ( 54) SS BOND : angle 0.74780 / 0.49 ( 108) hydrogen bonds : bond 0.03950 / 2.65 ( 1490) hydrogen bonds : angle 5.40991 / 3.78 ( 4200) link_BETA1-4 : bond 0.00497 / 0.33 ( 18) link_BETA1-4 : angle 1.10865 / 0.74 ( 54) link_BETA1-6 : bond 0.00279 / 0.17 ( 6) link_BETA1-6 : angle 1.30874 / 0.81 ( 18) link_NAG-ASN : bond 0.00613 / 0.35 ( 54) link_NAG-ASN : angle 2.21807 / 1.37 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 396 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7276 (mp) REVERT: A 129 LYS cc_start: 0.7939 (mmtt) cc_final: 0.7686 (tptp) REVERT: A 307 THR cc_start: 0.8851 (t) cc_final: 0.8562 (m) REVERT: A 697 MET cc_start: 0.8497 (ptm) cc_final: 0.8198 (ptm) REVERT: A 702 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: A 747 THR cc_start: 0.8697 (m) cc_final: 0.8321 (p) REVERT: D 75 THR cc_start: 0.7883 (m) cc_final: 0.7583 (t) REVERT: E 48 MET cc_start: 0.8912 (mtp) cc_final: 0.8540 (mtp) REVERT: B 207 HIS cc_start: 0.7611 (t70) cc_final: 0.7122 (m90) REVERT: B 224 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: B 307 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8326 (m) REVERT: B 324 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: B 814 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7718 (mmtm) REVERT: C 24 ARG cc_start: 0.7616 (ttp-110) cc_final: 0.6978 (mmp-170) REVERT: F 82 GLU cc_start: 0.7814 (tp30) cc_final: 0.7606 (mm-30) REVERT: K 81 ASN cc_start: 0.7391 (p0) cc_final: 0.7173 (p0) REVERT: K 207 HIS cc_start: 0.7318 (t-90) cc_final: 0.6753 (m90) REVERT: K 287 ASP cc_start: 0.8029 (t0) cc_final: 0.7554 (t70) REVERT: K 616 ASN cc_start: 0.7595 (t0) cc_final: 0.7241 (t0) REVERT: K 619 GLU cc_start: 0.7609 (mp0) cc_final: 0.7075 (mp0) REVERT: K 644 GLN cc_start: 0.8783 (tp40) cc_final: 0.8453 (tp-100) REVERT: K 1138 TYR cc_start: 0.7985 (t80) cc_final: 0.7766 (t80) REVERT: L 34 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8388 (tm) REVERT: M 43 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7304 (mt0) REVERT: M 70 MET cc_start: 0.7992 (mtt) cc_final: 0.7685 (mtt) outliers start: 83 outliers final: 59 residues processed: 448 average time/residue: 0.6622 time to fit residues: 361.1080 Evaluate side-chains 449 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 382 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 359 SER Chi-restraints excluded: chain K residue 427 ASP Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 586 ASP Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 772 VAL Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 379 optimal weight: 0.6980 chunk 229 optimal weight: 0.7980 chunk 302 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 397 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 305 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 312 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 157 optimal weight: 0.0770 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 779 GLN A 935 GLN A1101 HIS ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN B 121 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN K 394 ASN ** K 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1005 GLN ** K1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.193910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.160191 restraints weight = 36354.767| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.10 r_work: 0.3430 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 35241 Z= 0.177 Angle : 0.699 59.199 48282 Z= 0.368 Chirality : 0.067 3.379 5685 Planarity : 0.005 0.126 6177 Dihedral : 4.234 30.338 4860 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.39 % Allowed : 14.17 % Favored : 83.44 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 0.90 (0.12), residues: 4497 helix: 2.37 (0.20), residues: 651 sheet: 0.73 (0.13), residues: 1425 loop : 0.09 (0.13), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG K 346 TYR 0.019 0.001 TYR C 92 PHE 0.028 0.002 PHE K 592 TRP 0.014 0.002 TRP E 106 HIS 0.005 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (35109) covalent geometry : angle 0.66814 / 0.36 (47940) SS BOND : bond 0.00250 / 0.17 ( 54) SS BOND : angle 0.77976 / 0.50 ( 108) hydrogen bonds : bond 0.03979 / 2.67 ( 1490) hydrogen bonds : angle 5.41043 / 3.78 ( 4200) link_BETA1-4 : bond 0.00463 / 0.32 ( 18) link_BETA1-4 : angle 1.12906 / 0.77 ( 54) link_BETA1-6 : bond 0.00459 / 0.26 ( 6) link_BETA1-6 : angle 1.36670 / 0.85 ( 18) link_NAG-ASN : bond 0.01117 / 0.50 ( 54) link_NAG-ASN : angle 3.52482 / 2.22 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15847.83 seconds wall clock time: 269 minutes 23.54 seconds (16163.54 seconds total)