Starting phenix.real_space_refine on Mon Sep 23 22:03:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/09_2024/7vy2_32192.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/09_2024/7vy2_32192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/09_2024/7vy2_32192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/09_2024/7vy2_32192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/09_2024/7vy2_32192.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/09_2024/7vy2_32192.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.000 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 52 5.49 5 Mg 64 5.21 5 S 171 5.16 5 C 32638 2.51 5 N 6181 2.21 5 O 7184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 46292 Number of models: 1 Model: "" Number of chains: 131 Chain: "L" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2233 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2437 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 293} Chain: "H" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1884 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 224} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 386 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "I" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 453 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 448 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'FME:plan-2': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "V" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 451 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "W" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "1" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "5" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "6" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 332 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "7" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 415 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "8" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "X" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 478 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "U" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 353 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "l" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2233 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "m" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2437 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 293} Chain: "h" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1884 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 224} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 386 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "d" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "i" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "k" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "o" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 453 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "q" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "s" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 454 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "v" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'FME:plan-2': 1, 'FME:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "w" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "y" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'FME:plan-2': 1, 'FME:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "z" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "01" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "02" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "03" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "04" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "05" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "06" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 332 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "07" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 415 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "08" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "x" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 456 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 54} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "u" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 71 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 12} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 482 Unusual residues: {'BCL': 2, 'BPH': 1, 'LMT': 2, 'PGV': 4, 'U10': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'PGV:plan-3': 3, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 51 Chain: "M" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 535 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CDL': 1, 'LMT': 4, 'PGV': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 185 Unusual residues: {'LMT': 1, 'PGV': 3, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 138 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'BCL': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'PGV': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 143 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 210 Unusual residues: {'BCL': 1, 'CDL': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 161 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Unusual residues: {'BCL': 1, 'CDL': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 6 Chain: "Z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "2" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SPO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "3" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 170 Unusual residues: {'BCL': 1, 'LMT': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "4" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 141 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "6" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 60 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Unusual residues: {'CDL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 9 Chain: "U" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {'LMT': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "l" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 345 Unusual residues: {'BCL': 1, 'BPH': 1, 'PGV': 4, 'U10': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'PGV:plan-3': 3, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 55 Chain: "m" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 634 Unusual residues: {' FE': 1, 'BCL': 3, 'BPH': 1, 'CDL': 2, 'LMT': 2, 'PGV': 2, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 2, 'CDL:plan-1': 1, 'U10:plan-10': 1} Unresolved non-hydrogen planarities: 12 Chain: "h" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 234 Unusual residues: {'CDL': 1, 'LMT': 2, 'PGV': 2, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 3 Chain: "b" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'BCL': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 27 Chain: "e" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 274 Unusual residues: {'BCL': 1, 'PGV': 2, 'PTY': 1, 'SPO': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "g" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 10 Chain: "j" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'BCL': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "n" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "o" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 166 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 205 Unusual residues: {'BCL': 1, 'LMT': 2, 'SPO': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 5 Chain: "t" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "w" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "y" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 211 Unusual residues: {'BCL': 1, 'CDL': 1, 'LDA': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "z" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "01" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "02" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "03" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 128 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "04" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "05" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "06" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "07" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "08" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'CDL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGV:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 21.34, per 1000 atoms: 0.46 Number of scatterers: 46292 At special positions: 0 Unit cell: (220.58, 163.18, 106.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 171 16.00 P 52 15.00 Mg 64 11.99 O 7184 8.00 N 6181 7.00 C 32638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=60, symmetry=0 Number of additional bonds: simple=60, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.96 Conformation dependent library (CDL) restraints added in 3.6 seconds 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8434 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 12 sheets defined 73.0% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'L' and resid 6 through 10 Processing helix chain 'L' and resid 32 through 57 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 83 through 112 Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.622A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 Processing helix chain 'L' and resid 151 through 163 Processing helix chain 'L' and resid 166 through 169 Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 221 Processing helix chain 'L' and resid 225 through 248 removed outlier: 3.777A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 262 Processing helix chain 'L' and resid 263 through 268 removed outlier: 3.839A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 29 Processing helix chain 'M' and resid 36 through 41 Processing helix chain 'M' and resid 53 through 78 removed outlier: 3.746A pdb=" N VAL M 57 " --> pdb=" O GLY M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 108 through 111 Processing helix chain 'M' and resid 112 through 140 removed outlier: 3.635A pdb=" N LEU M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 162 removed outlier: 3.792A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 Processing helix chain 'M' and resid 178 through 193 removed outlier: 3.558A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 257 removed outlier: 3.595A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 287 removed outlier: 3.530A pdb=" N ARG M 267 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'H' and resid 11 through 35 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 209 through 216 removed outlier: 3.828A pdb=" N PHE H 213 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 244 removed outlier: 3.628A pdb=" N GLY H 240 " --> pdb=" O TYR H 236 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 248 Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 12 through 38 removed outlier: 4.226A pdb=" N VAL A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 45 Processing helix chain 'D' and resid 3 through 10 Processing helix chain 'D' and resid 12 through 38 removed outlier: 3.545A pdb=" N VAL D 18 " --> pdb=" O ARG D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'E' and resid 12 through 45 Processing helix chain 'F' and resid 3 through 10 Processing helix chain 'F' and resid 12 through 38 Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'G' and resid 12 through 45 removed outlier: 3.514A pdb=" N GLN G 17 " --> pdb=" O ASP G 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 10 removed outlier: 3.880A pdb=" N LYS I 6 " --> pdb=" O LYS I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 38 Processing helix chain 'I' and resid 42 through 52 Processing helix chain 'J' and resid 12 through 45 Processing helix chain 'K' and resid 3 through 10 Processing helix chain 'K' and resid 12 through 38 Processing helix chain 'K' and resid 39 through 41 No H-bonds generated for 'chain 'K' and resid 39 through 41' Processing helix chain 'K' and resid 42 through 51 Processing helix chain 'N' and resid 12 through 45 Processing helix chain 'O' and resid 3 through 10 removed outlier: 3.600A pdb=" N LYS O 6 " --> pdb=" O LYS O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 38 Processing helix chain 'O' and resid 39 through 41 No H-bonds generated for 'chain 'O' and resid 39 through 41' Processing helix chain 'O' and resid 42 through 52 Processing helix chain 'P' and resid 14 through 45 removed outlier: 4.036A pdb=" N GLU P 18 " --> pdb=" O GLU P 14 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 10 Processing helix chain 'Q' and resid 12 through 38 removed outlier: 3.521A pdb=" N VAL Q 18 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 51 Processing helix chain 'R' and resid 12 through 45 Processing helix chain 'S' and resid 3 through 10 removed outlier: 3.865A pdb=" N LYS S 6 " --> pdb=" O LYS S 3 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 38 Processing helix chain 'S' and resid 42 through 51 Processing helix chain 'T' and resid 13 through 45 Processing helix chain 'V' and resid 3 through 10 removed outlier: 3.758A pdb=" N LYS V 6 " --> pdb=" O LYS V 3 " (cutoff:3.500A) Processing helix chain 'V' and resid 12 through 38 Processing helix chain 'V' and resid 42 through 51 Processing helix chain 'W' and resid 12 through 45 Processing helix chain 'Y' and resid 3 through 8 removed outlier: 3.540A pdb=" N ILE Y 7 " --> pdb=" O PHE Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 38 Processing helix chain 'Y' and resid 39 through 41 No H-bonds generated for 'chain 'Y' and resid 39 through 41' Processing helix chain 'Y' and resid 42 through 51 Processing helix chain 'Z' and resid 12 through 45 Processing helix chain '1' and resid 3 through 10 removed outlier: 4.001A pdb=" N LYS 1 6 " --> pdb=" O LYS 1 3 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP 1 8 " --> pdb=" O TYR 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 12 through 38 removed outlier: 3.680A pdb=" N VAL 1 18 " --> pdb=" O ARG 1 14 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 52 Processing helix chain '2' and resid 12 through 45 Processing helix chain '3' and resid 1 through 5 removed outlier: 3.837A pdb=" N TYR 3 5 " --> pdb=" O SER 3 2 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 11 Processing helix chain '3' and resid 12 through 38 removed outlier: 3.801A pdb=" N THR 3 38 " --> pdb=" O ILE 3 34 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 52 Processing helix chain '4' and resid 12 through 45 Processing helix chain '5' and resid 3 through 9 removed outlier: 4.076A pdb=" N LYS 5 6 " --> pdb=" O LYS 5 3 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 38 Processing helix chain '5' and resid 39 through 41 No H-bonds generated for 'chain '5' and resid 39 through 41' Processing helix chain '5' and resid 42 through 51 Processing helix chain '6' and resid 12 through 45 Processing helix chain '7' and resid 6 through 11 Processing helix chain '7' and resid 12 through 38 Processing helix chain '7' and resid 42 through 51 Processing helix chain '8' and resid 12 through 45 Processing helix chain 'X' and resid 14 through 54 removed outlier: 3.623A pdb=" N ASN X 18 " --> pdb=" O ASN X 14 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 30 Processing helix chain 'U' and resid 31 through 49 removed outlier: 3.725A pdb=" N GLY U 35 " --> pdb=" O HIS U 31 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR U 49 " --> pdb=" O PHE U 45 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 10 Processing helix chain 'l' and resid 32 through 57 Processing helix chain 'l' and resid 70 through 74 Processing helix chain 'l' and resid 83 through 112 removed outlier: 3.578A pdb=" N GLN l 87 " --> pdb=" O GLY l 83 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 133 Processing helix chain 'l' and resid 133 through 139 Processing helix chain 'l' and resid 141 through 145 Processing helix chain 'l' and resid 152 through 163 Processing helix chain 'l' and resid 164 through 165 No H-bonds generated for 'chain 'l' and resid 164 through 165' Processing helix chain 'l' and resid 166 through 169 Processing helix chain 'l' and resid 170 through 199 Processing helix chain 'l' and resid 208 through 221 Processing helix chain 'l' and resid 225 through 250 removed outlier: 3.847A pdb=" N HIS l 230 " --> pdb=" O THR l 226 " (cutoff:3.500A) Processing helix chain 'l' and resid 258 through 262 Processing helix chain 'l' and resid 263 through 268 removed outlier: 3.722A pdb=" N VAL l 267 " --> pdb=" O TRP l 263 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 41 Processing helix chain 'm' and resid 53 through 78 Processing helix chain 'm' and resid 81 through 88 Processing helix chain 'm' and resid 98 through 102 Processing helix chain 'm' and resid 108 through 111 Processing helix chain 'm' and resid 112 through 140 Processing helix chain 'm' and resid 144 through 162 removed outlier: 3.665A pdb=" N ALA m 153 " --> pdb=" O ALA m 149 " (cutoff:3.500A) Processing helix chain 'm' and resid 162 through 169 Processing helix chain 'm' and resid 170 through 174 Processing helix chain 'm' and resid 178 through 193 removed outlier: 3.741A pdb=" N LEU m 183 " --> pdb=" O ILE m 179 " (cutoff:3.500A) Processing helix chain 'm' and resid 195 through 198 Processing helix chain 'm' and resid 199 through 226 Processing helix chain 'm' and resid 227 through 230 Processing helix chain 'm' and resid 233 through 240 Processing helix chain 'm' and resid 242 through 257 Processing helix chain 'm' and resid 263 through 287 removed outlier: 3.635A pdb=" N ARG m 267 " --> pdb=" O GLU m 263 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) Processing helix chain 'm' and resid 293 through 301 Processing helix chain 'h' and resid 11 through 35 Processing helix chain 'h' and resid 103 through 108 Processing helix chain 'h' and resid 109 through 113 Processing helix chain 'h' and resid 194 through 196 No H-bonds generated for 'chain 'h' and resid 194 through 196' Processing helix chain 'h' and resid 209 through 213 removed outlier: 3.756A pdb=" N PHE h 213 " --> pdb=" O SER h 210 " (cutoff:3.500A) Processing helix chain 'h' and resid 226 through 244 removed outlier: 3.916A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 10 removed outlier: 3.536A pdb=" N TYR a 5 " --> pdb=" O SER a 2 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 38 removed outlier: 4.597A pdb=" N VAL a 18 " --> pdb=" O ARG a 14 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 45 Processing helix chain 'd' and resid 2 through 10 removed outlier: 4.186A pdb=" N TYR d 5 " --> pdb=" O SER d 2 " (cutoff:3.500A) Processing helix chain 'd' and resid 12 through 38 removed outlier: 4.241A pdb=" N VAL d 18 " --> pdb=" O ARG d 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 42 through 51 Processing helix chain 'e' and resid 12 through 45 Processing helix chain 'f' and resid 1 through 10 removed outlier: 3.513A pdb=" N PHE f 4 " --> pdb=" O FME f 1 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR f 5 " --> pdb=" O SER f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 38 Processing helix chain 'f' and resid 42 through 51 Processing helix chain 'g' and resid 12 through 45 Processing helix chain 'i' and resid 6 through 11 removed outlier: 3.573A pdb=" N ILE i 10 " --> pdb=" O LYS i 6 " (cutoff:3.500A) Processing helix chain 'i' and resid 12 through 38 Processing helix chain 'i' and resid 42 through 51 Processing helix chain 'j' and resid 12 through 45 Processing helix chain 'k' and resid 1 through 10 removed outlier: 3.608A pdb=" N PHE k 4 " --> pdb=" O FME k 1 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR k 5 " --> pdb=" O SER k 2 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 38 Processing helix chain 'k' and resid 42 through 51 Processing helix chain 'n' and resid 12 through 45 Processing helix chain 'o' and resid 1 through 5 removed outlier: 4.119A pdb=" N TYR o 5 " --> pdb=" O SER o 2 " (cutoff:3.500A) Processing helix chain 'o' and resid 6 through 11 removed outlier: 3.878A pdb=" N ILE o 10 " --> pdb=" O LYS o 6 " (cutoff:3.500A) Processing helix chain 'o' and resid 12 through 38 Processing helix chain 'o' and resid 42 through 51 Processing helix chain 'p' and resid 14 through 45 removed outlier: 3.597A pdb=" N GLU p 18 " --> pdb=" O GLU p 14 " (cutoff:3.500A) Processing helix chain 'q' and resid 4 through 10 Processing helix chain 'q' and resid 12 through 38 Processing helix chain 'q' and resid 42 through 51 Processing helix chain 'r' and resid 12 through 45 Processing helix chain 's' and resid 4 through 10 Processing helix chain 's' and resid 12 through 38 Processing helix chain 's' and resid 42 through 51 Processing helix chain 't' and resid 12 through 45 Processing helix chain 'v' and resid 3 through 10 removed outlier: 3.957A pdb=" N LYS v 6 " --> pdb=" O LYS v 3 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE v 7 " --> pdb=" O PHE v 4 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP v 8 " --> pdb=" O TYR v 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 12 through 38 Processing helix chain 'v' and resid 42 through 51 Processing helix chain 'w' and resid 12 through 45 removed outlier: 4.213A pdb=" N VAL w 22 " --> pdb=" O GLU w 18 " (cutoff:3.500A) Processing helix chain 'y' and resid 2 through 4 No H-bonds generated for 'chain 'y' and resid 2 through 4' Processing helix chain 'y' and resid 5 through 11 removed outlier: 3.637A pdb=" N MET y 9 " --> pdb=" O TYR y 5 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 38 Processing helix chain 'y' and resid 39 through 41 No H-bonds generated for 'chain 'y' and resid 39 through 41' Processing helix chain 'y' and resid 42 through 51 Processing helix chain 'z' and resid 12 through 45 Processing helix chain '01' and resid 3 through 10 removed outlier: 4.052A pdb=" N LYS01 6 " --> pdb=" O LYS01 3 " (cutoff:3.500A) Processing helix chain '01' and resid 12 through 38 Processing helix chain '01' and resid 42 through 51 Processing helix chain '02' and resid 12 through 45 removed outlier: 3.531A pdb=" N LEU02 29 " --> pdb=" O SER02 25 " (cutoff:3.500A) Processing helix chain '03' and resid 3 through 5 No H-bonds generated for 'chain '03' and resid 3 through 5' Processing helix chain '03' and resid 6 through 11 removed outlier: 3.590A pdb=" N ILE03 10 " --> pdb=" O LYS03 6 " (cutoff:3.500A) Processing helix chain '03' and resid 12 through 38 Processing helix chain '03' and resid 42 through 52 Processing helix chain '04' and resid 12 through 45 Processing helix chain '05' and resid 3 through 10 removed outlier: 3.705A pdb=" N LYS05 6 " --> pdb=" O LYS05 3 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE05 10 " --> pdb=" O ILE05 7 " (cutoff:3.500A) Processing helix chain '05' and resid 12 through 38 Processing helix chain '05' and resid 42 through 52 Processing helix chain '06' and resid 12 through 45 Processing helix chain '07' and resid 6 through 11 Processing helix chain '07' and resid 12 through 38 Processing helix chain '07' and resid 42 through 51 Processing helix chain '08' and resid 12 through 45 Processing helix chain 'x' and resid 14 through 55 removed outlier: 3.502A pdb=" N ARG x 20 " --> pdb=" O LYS x 16 " (cutoff:3.500A) Processing helix chain 'u' and resid 56 through 61 Processing sheet with id=AA1, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.641A pdb=" N PHE L 24 " --> pdb=" O VAL L 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.733A pdb=" N ALA H 144 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG M 13 " --> pdb=" O VAL H 142 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL H 142 " --> pdb=" O ARG M 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 62 through 65 Processing sheet with id=AA4, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA5, first strand: chain 'H' and resid 131 through 133 removed outlier: 5.711A pdb=" N VAL H 164 " --> pdb=" O GLU H 182 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU H 182 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP H 166 " --> pdb=" O GLU H 180 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP H 170 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA H 176 " --> pdb=" O ASP H 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.899A pdb=" N VAL H 153 " --> pdb=" O ALA H 161 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL H 205 " --> pdb=" O PRO H 152 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG H 154 " --> pdb=" O VAL H 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'l' and resid 24 through 26 removed outlier: 3.681A pdb=" N PHE l 24 " --> pdb=" O VAL l 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'm' and resid 11 through 13 removed outlier: 6.435A pdb=" N GLN m 11 " --> pdb=" O SER h 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'h' and resid 62 through 65 Processing sheet with id=AB1, first strand: chain 'h' and resid 87 through 89 Processing sheet with id=AB2, first strand: chain 'h' and resid 131 through 133 removed outlier: 5.491A pdb=" N VAL h 164 " --> pdb=" O GLU h 182 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU h 182 " --> pdb=" O VAL h 164 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP h 166 " --> pdb=" O GLU h 180 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ASP h 170 " --> pdb=" O ALA h 176 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ALA h 176 " --> pdb=" O ASP h 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 131 through 133 removed outlier: 6.601A pdb=" N VAL h 153 " --> pdb=" O ALA h 161 " (cutoff:3.500A) 2550 hydrogen bonds defined for protein. 7242 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: 11.52 Time building geometry restraints manager: 10.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 13568 1.37 - 1.54: 33452 1.54 - 1.71: 384 1.71 - 1.88: 332 1.88 - 2.05: 256 Bond restraints: 47992 Sorted by residual: bond pdb=" CA7 CDL m 410 " pdb=" OA8 CDL m 410 " ideal model delta sigma weight residual 1.334 1.458 -0.124 1.10e-02 8.26e+03 1.28e+02 bond pdb=" CA7 CDL y 102 " pdb=" OA8 CDL y 102 " ideal model delta sigma weight residual 1.334 1.458 -0.124 1.10e-02 8.26e+03 1.27e+02 bond pdb=" CA7 CDL h 805 " pdb=" OA8 CDL h 805 " ideal model delta sigma weight residual 1.334 1.457 -0.123 1.10e-02 8.26e+03 1.26e+02 bond pdb=" CA7 CDL X 101 " pdb=" OA8 CDL X 101 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" CA7 CDL K 401 " pdb=" OA8 CDL K 401 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.22e+02 ... (remaining 47987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 60805 3.74 - 7.47: 4076 7.47 - 11.21: 594 11.21 - 14.95: 113 14.95 - 18.69: 27 Bond angle restraints: 65615 Sorted by residual: angle pdb=" C1D BCL f 102 " pdb=" C2D BCL f 102 " pdb=" CMD BCL f 102 " ideal model delta sigma weight residual 125.57 140.61 -15.04 1.83e+00 2.99e-01 6.77e+01 angle pdb=" C1D BCL a 101 " pdb=" C2D BCL a 101 " pdb=" CMD BCL a 101 " ideal model delta sigma weight residual 125.57 140.05 -14.48 1.83e+00 2.99e-01 6.27e+01 angle pdb=" C1D BCL d 101 " pdb=" C2D BCL d 101 " pdb=" CMD BCL d 101 " ideal model delta sigma weight residual 125.57 139.82 -14.24 1.83e+00 2.99e-01 6.07e+01 angle pdb=" C1D BCL b 101 " pdb=" C2D BCL b 101 " pdb=" CMD BCL b 101 " ideal model delta sigma weight residual 125.57 139.76 -14.19 1.83e+00 2.99e-01 6.02e+01 angle pdb=" C1D BCL o 101 " pdb=" C2D BCL o 101 " pdb=" CMD BCL o 101 " ideal model delta sigma weight residual 125.57 139.76 -14.19 1.83e+00 2.99e-01 6.02e+01 ... (remaining 65610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 25320 35.98 - 71.96: 1307 71.96 - 107.94: 232 107.94 - 143.92: 67 143.92 - 179.89: 18 Dihedral angle restraints: 26944 sinusoidal: 13827 harmonic: 13117 Sorted by residual: dihedral pdb=" C1 BCL a 101 " pdb=" CGA BCL a 101 " pdb=" O2A BCL a 101 " pdb=" CBA BCL a 101 " ideal model delta sinusoidal sigma weight residual 180.00 73.33 106.67 1 6.00e+00 2.78e-02 3.43e+02 dihedral pdb=" C1 BCL M 401 " pdb=" C2 BCL M 401 " pdb=" C3 BCL M 401 " pdb=" C5 BCL M 401 " ideal model delta sinusoidal sigma weight residual -180.00 -0.29 -179.71 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL m 402 " pdb=" C2 BCL m 402 " pdb=" C3 BCL m 402 " pdb=" C5 BCL m 402 " ideal model delta sinusoidal sigma weight residual -180.00 -0.94 -179.06 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 26941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 5305 0.064 - 0.128: 895 0.128 - 0.192: 206 0.192 - 0.256: 41 0.256 - 0.320: 20 Chirality restraints: 6467 Sorted by residual: chirality pdb=" C3C BPH l 302 " pdb=" C2C BPH l 302 " pdb=" C4C BPH l 302 " pdb=" CAC BPH l 302 " both_signs ideal model delta sigma weight residual False 2.83 2.52 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C05 PGV h 801 " pdb=" C04 PGV h 801 " pdb=" C06 PGV h 801 " pdb=" O05 PGV h 801 " both_signs ideal model delta sigma weight residual False 2.29 2.59 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C05 PGV q 102 " pdb=" C04 PGV q 102 " pdb=" C06 PGV q 102 " pdb=" O05 PGV q 102 " both_signs ideal model delta sigma weight residual False 2.29 2.59 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 6464 not shown) Planarity restraints: 7851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL Z 101 " 0.371 3.00e-02 1.11e+03 3.06e-01 5.21e+02 pdb=" CBA BCL Z 101 " 0.157 3.00e-02 1.11e+03 pdb=" CGA BCL Z 101 " -0.083 3.00e-02 1.11e+03 pdb=" O1A BCL Z 101 " 0.094 3.00e-02 1.11e+03 pdb=" O2A BCL Z 101 " -0.539 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL a 101 " -0.347 3.00e-02 1.11e+03 2.92e-01 4.73e+02 pdb=" CBA BCL a 101 " -0.033 3.00e-02 1.11e+03 pdb=" CGA BCL a 101 " 0.062 3.00e-02 1.11e+03 pdb=" O1A BCL a 101 " -0.195 3.00e-02 1.11e+03 pdb=" O2A BCL a 101 " 0.512 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BCL 7 101 " -0.230 3.10e-02 1.04e+03 2.86e-01 4.27e+02 pdb=" C4C BCL 7 101 " -0.199 3.10e-02 1.04e+03 pdb=" CHC BCL 7 101 " -0.056 3.10e-02 1.04e+03 pdb=" CHD BCL 7 101 " -0.071 3.10e-02 1.04e+03 pdb=" NC BCL 7 101 " 0.556 3.10e-02 1.04e+03 ... (remaining 7848 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 291 2.53 - 3.13: 32939 3.13 - 3.72: 76885 3.72 - 4.31: 113533 4.31 - 4.90: 183245 Nonbonded interactions: 406893 Sorted by model distance: nonbonded pdb=" OE2 GLU m 234 " pdb="FE FE m 405 " model vdw 1.943 2.260 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 404 " model vdw 1.964 2.260 nonbonded pdb=" CE1 HIS e 38 " pdb="MG BCL e 102 " model vdw 1.989 3.130 nonbonded pdb=" O ALA L 78 " pdb=" O3' LMT L 305 " model vdw 2.026 3.040 nonbonded pdb=" CE1 HIS E 38 " pdb="MG BCL E 101 " model vdw 2.103 3.130 ... (remaining 406888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '01' and ((resid 4 through 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain '03' and ((resid 4 through 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain '05' and ((resid 4 through 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain '07' and (resid 4 through 10 or (resid 11 and (name N or name CA or name \ C or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or nam \ e CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain '1' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain '3' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain '5' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain '7' and (resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 54)) selection = (chain 'F' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'I' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'K' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'O' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'Q' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'S' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 53 or (resid 54 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'V' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 53 or (resid 54 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'Y' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'd' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 54)) selection = (chain 'f' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'i' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'k' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'o' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'q' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 's' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'v' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'y' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain '02' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or nam \ e CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '04' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or nam \ e CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '06' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or nam \ e CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '08' and resid 11 through 48) selection = (chain '2' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '4' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '6' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '8' and resid 11 through 48) selection = (chain 'B' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'E' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'G' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'J' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'N' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'P' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'R' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'T' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'W' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'Z' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'b' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'e' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'g' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'j' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'n' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'p' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'r' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 't' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'w' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'z' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) } ncs_group { reference = (chain 'A' and resid 1 through 45) selection = (chain 'a' and resid 1 through 45) } ncs_group { reference = (chain 'H' and (resid 1 through 248 or resid 801 or (resid 802 and (name C1 or n \ ame C1' or name C10 or name C11 or name C12 or name C1B or name C2 or name C2' o \ r name C2B or name C3 or name C3' or name C4 or name C4' or name C5 or name C5' \ or name C6 or name C6' or name C7 or name C8 or name C9 or name O1' or name O1B \ or name O2' or name O3' or name O5' or name O5B or name O6')))) selection = (chain 'h' and (resid 1 through 248 or resid 801 through 802)) } ncs_group { reference = (chain 'L' and (resid 1 through 281 or resid 301 through 304 or (resid 307 and ( \ name C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C1 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C \ 3 or name C4 or name C5 or name C6 or name C7 or name C8 or name O01 or name O02 \ or name O03 or name O04 or name O05 or name O06 or name O11 or name O12 or name \ O13 or name O14 or name P )) or (resid 308 and (name C01 or name C02 or name C0 \ 3 or name C04 or name C05 or name C06 or name C1 or name C19 or name C2 or name \ C20 or name C21 or name C3 or name C4 or name O01 or name O02 or name O03 or nam \ e O04 or name O05 or name O06 or name O11 or name O12 or name O13 or name O14 or \ name P )))) selection = (chain 'l' and (resid 1 through 281 or resid 301 through 304 or resid 307 throug \ h 308)) } ncs_group { reference = (chain 'M' and (resid 1 through 306 or resid 401 through 402 or resid 408 throug \ h 411)) selection = (chain 'm' and (resid 1 through 306 or resid 401 through 402 or (resid 408 and ( \ name C1 or name C1' or name C10 or name C11 or name C12 or name C1B or name C2 o \ r name C2' or name C3 or name C3' or name C4 or name C4' or name C5 or name C5' \ or name C6 or name C6' or name C7 or name C8 or name C9 or name O1' or name O1B \ or name O2' or name O3' or name O5' or name O6')) or resid 409 through 411)) } ncs_group { reference = (chain 'X' and (resid 10 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 69 or (resid 102 and (name CB2 or \ name OB2 or name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name CA2 or name CA3 or name CA4 or name \ CA5 or name O1 or name OA2 or name OA3 or name OA4 or name OA5 or name OA6 or na \ me OA7 or name OB4 or name OB5 or name PA1 or name PB2)))) selection = (chain 'x' and (resid 10 through 69 or resid 102)) } 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: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.370 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 73.010 Find NCS groups from input model: 2.830 Set up NCS constraints: 0.180 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.019 0.183 47992 Z= 1.004 Angle : 1.910 18.686 65615 Z= 0.825 Chirality : 0.056 0.320 6467 Planarity : 0.018 0.306 7851 Dihedral : 21.907 179.895 18510 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.39 % Allowed : 6.92 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.12), residues: 4376 helix: 1.75 (0.09), residues: 2932 sheet: -0.67 (0.65), residues: 62 loop : -0.25 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 157 HIS 0.010 0.002 HIS L 153 PHE 0.021 0.002 PHE O 23 TYR 0.018 0.002 TYR I 51 ARG 0.006 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 916 time to evaluate : 3.359 Fit side-chains REVERT: M 20 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6484 (mmm) REVERT: M 60 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7264 (mm) REVERT: M 214 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8951 (tt) REVERT: M 263 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: M 306 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7895 (mp) REVERT: B 20 HIS cc_start: 0.6593 (t-90) cc_final: 0.6351 (t70) REVERT: I 54 VAL cc_start: 0.7018 (p) cc_final: 0.6663 (t) REVERT: O 20 GLN cc_start: 0.7015 (mt0) cc_final: 0.6805 (pt0) REVERT: S 15 ARG cc_start: 0.4970 (tmm160) cc_final: 0.4150 (mtt180) REVERT: T 17 GLN cc_start: 0.6710 (mm110) cc_final: 0.6509 (mt0) REVERT: V 4 PHE cc_start: 0.5817 (m-80) cc_final: 0.5448 (m-80) REVERT: V 9 MET cc_start: 0.3549 (ttp) cc_final: 0.3143 (tmm) REVERT: W 42 TYR cc_start: 0.5602 (t80) cc_final: 0.5345 (t80) REVERT: 1 9 MET cc_start: 0.4219 (mtt) cc_final: 0.3841 (mmm) REVERT: 3 9 MET cc_start: 0.2292 (mtp) cc_final: 0.2003 (tpt) REVERT: 3 11 PHE cc_start: 0.4131 (OUTLIER) cc_final: 0.3873 (m-80) REVERT: 3 25 PHE cc_start: 0.7473 (t80) cc_final: 0.7174 (t80) REVERT: 3 36 LEU cc_start: 0.8570 (mt) cc_final: 0.8343 (mp) REVERT: 5 10 ILE cc_start: 0.5479 (pt) cc_final: 0.5259 (pp) REVERT: 5 15 ARG cc_start: 0.4740 (ptp-110) cc_final: 0.4398 (ttp80) REVERT: 5 39 PRO cc_start: 0.5542 (Cg_endo) cc_final: 0.5158 (Cg_exo) REVERT: 8 24 MET cc_start: 0.5023 (mmm) cc_final: 0.4568 (mmt) REVERT: X 29 LYS cc_start: 0.7872 (mtpp) cc_final: 0.7663 (mtpp) REVERT: U 13 MET cc_start: 0.5149 (mmm) cc_final: 0.4889 (mmm) REVERT: l 72 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6352 (pp20) REVERT: m 236 GLU cc_start: 0.7556 (tp30) cc_final: 0.7321 (tp30) REVERT: m 263 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: v 17 PHE cc_start: 0.7317 (m-80) cc_final: 0.7026 (t80) REVERT: 05 39 PRO cc_start: 0.7059 (Cg_endo) cc_final: 0.6631 (Cg_exo) REVERT: 06 24 MET cc_start: 0.6736 (mmm) cc_final: 0.6276 (ptp) REVERT: 06 47 TRP cc_start: 0.6418 (p90) cc_final: 0.6047 (p90) outliers start: 126 outliers final: 48 residues processed: 991 average time/residue: 0.9713 time to fit residues: 1271.6909 Evaluate side-chains 806 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 750 time to evaluate : 5.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain M residue 306 LEU Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain 1 residue 12 ASP Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 3 residue 11 PHE Chi-restraints excluded: chain X residue 57 ILE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 267 VAL Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain m residue 263 GLU Chi-restraints excluded: chain h residue 175 MET Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 20 GLN Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain r residue 25 SER Chi-restraints excluded: chain s residue 40 SER Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain t residue 12 THR Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain 03 residue 29 VAL Chi-restraints excluded: chain 03 residue 37 SER Chi-restraints excluded: chain 06 residue 11 LEU Chi-restraints excluded: chain 07 residue 54 VAL Chi-restraints excluded: chain x residue 66 ASN Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 0.9990 chunk 325 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 336 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 250 optimal weight: 0.7980 chunk 389 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 173 HIS L 183 ASN M 301 HIS A 20 GLN B 17 GLN ** B 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 HIS F 20 GLN G 15 GLN G 17 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 17 GLN W 17 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 15 GLN 5 20 GLN 6 15 GLN ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 20 GLN X 66 ASN l 199 ASN m 259 ASN m 301 HIS h 44 ASN h 199 GLN h 206 ASN a 20 GLN ** d 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 HIS ** e 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN q 20 GLN r 20 HIS ** v 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 15 GLN w 17 GLN y 52 ASN ** 01 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 01 42 ASN 02 17 GLN 04 17 GLN 04 20 HIS ** 07 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 60 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 47992 Z= 0.185 Angle : 0.755 14.748 65615 Z= 0.297 Chirality : 0.040 0.250 6467 Planarity : 0.004 0.056 7851 Dihedral : 20.046 179.332 10819 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.91 % Allowed : 13.87 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.12), residues: 4376 helix: 2.35 (0.09), residues: 2878 sheet: -0.21 (0.77), residues: 46 loop : -0.14 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP g 44 HIS 0.017 0.001 HIS N 20 PHE 0.025 0.001 PHE L 216 TYR 0.016 0.001 TYR F 51 ARG 0.004 0.000 ARG05 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 836 time to evaluate : 3.280 Fit side-chains revert: symmetry clash REVERT: L 243 PHE cc_start: 0.7410 (m-10) cc_final: 0.7108 (m-10) REVERT: M 20 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6368 (mmm) REVERT: M 60 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7186 (mm) REVERT: M 138 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6462 (tp40) REVERT: S 15 ARG cc_start: 0.4911 (tmm160) cc_final: 0.4106 (mtt180) REVERT: S 45 GLU cc_start: 0.7316 (pt0) cc_final: 0.7014 (pt0) REVERT: T 29 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7986 (tp) REVERT: V 4 PHE cc_start: 0.5926 (m-80) cc_final: 0.5572 (m-80) REVERT: V 9 MET cc_start: 0.3541 (ttp) cc_final: 0.3027 (tmm) REVERT: W 42 TYR cc_start: 0.5700 (t80) cc_final: 0.5464 (t80) REVERT: 1 9 MET cc_start: 0.4202 (mtt) cc_final: 0.3662 (mmm) REVERT: 1 27 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6880 (mm) REVERT: 1 31 ILE cc_start: 0.7783 (mp) cc_final: 0.7362 (mt) REVERT: 3 25 PHE cc_start: 0.7624 (t80) cc_final: 0.7115 (t80) REVERT: 3 46 ILE cc_start: 0.7277 (pt) cc_final: 0.6988 (pp) REVERT: 5 15 ARG cc_start: 0.4819 (ptp-110) cc_final: 0.4531 (ttp80) REVERT: 7 45 GLU cc_start: 0.5212 (mm-30) cc_final: 0.4719 (tp30) REVERT: 8 24 MET cc_start: 0.4909 (mmm) cc_final: 0.4494 (mmt) REVERT: U 13 MET cc_start: 0.4963 (mmm) cc_final: 0.4713 (mmm) REVERT: l 72 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7039 (pp20) REVERT: h 173 GLU cc_start: 0.6582 (tp30) cc_final: 0.6374 (tp30) REVERT: n 42 TYR cc_start: 0.8006 (t80) cc_final: 0.7804 (t80) REVERT: v 17 PHE cc_start: 0.7249 (m-80) cc_final: 0.7011 (t80) REVERT: y 12 ASP cc_start: 0.7848 (t0) cc_final: 0.7582 (t70) REVERT: z 19 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6425 (tp) REVERT: z 39 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7558 (tp) REVERT: 01 8 TRP cc_start: 0.7322 (m100) cc_final: 0.6952 (m100) REVERT: 01 9 MET cc_start: 0.6482 (OUTLIER) cc_final: 0.6210 (mtm) REVERT: 05 39 PRO cc_start: 0.6910 (Cg_endo) cc_final: 0.6399 (Cg_exo) REVERT: 06 24 MET cc_start: 0.6702 (mmm) cc_final: 0.6224 (ptp) REVERT: 06 47 TRP cc_start: 0.6302 (p90) cc_final: 0.5974 (p90) outliers start: 145 outliers final: 47 residues processed: 911 average time/residue: 0.9518 time to fit residues: 1150.1309 Evaluate side-chains 801 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 745 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain T residue 35 ILE Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 2 residue 38 HIS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain j residue 39 LEU Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain t residue 12 THR Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 19 LEU Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 31 SER Chi-restraints excluded: chain z residue 39 LEU Chi-restraints excluded: chain 01 residue 9 MET Chi-restraints excluded: chain 02 residue 39 LEU Chi-restraints excluded: chain 03 residue 37 SER Chi-restraints excluded: chain 04 residue 21 SER Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain x residue 66 ASN Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 324 optimal weight: 0.9990 chunk 265 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 390 optimal weight: 3.9990 chunk 421 optimal weight: 10.0000 chunk 347 optimal weight: 7.9990 chunk 387 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 313 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 126 HIS A 42 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN O 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN ** R 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN m 81 ASN h 52 ASN a 20 GLN ** g 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN q 20 GLN ** v 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 01 20 GLN 01 42 ASN ** 07 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 47992 Z= 0.407 Angle : 0.870 17.248 65615 Z= 0.350 Chirality : 0.045 0.253 6467 Planarity : 0.005 0.057 7851 Dihedral : 19.777 179.900 10765 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.06 % Allowed : 16.19 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.12), residues: 4376 helix: 1.91 (0.09), residues: 2874 sheet: -0.21 (0.62), residues: 66 loop : -0.35 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP g 44 HIS 0.013 0.002 HIS B 38 PHE 0.026 0.002 PHE L 216 TYR 0.020 0.002 TYR m 198 ARG 0.007 0.001 ARG05 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 779 time to evaluate : 3.245 Fit side-chains REVERT: L 2 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8718 (mt) REVERT: M 20 MET cc_start: 0.6935 (mmm) cc_final: 0.6252 (mmm) REVERT: M 60 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7357 (mm) REVERT: M 138 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6554 (tp40) REVERT: M 214 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8981 (tt) REVERT: M 263 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: Q 20 GLN cc_start: 0.7105 (mm110) cc_final: 0.6802 (tp40) REVERT: S 15 ARG cc_start: 0.5242 (tmm160) cc_final: 0.4170 (mtt180) REVERT: T 29 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8063 (tt) REVERT: V 4 PHE cc_start: 0.6002 (m-80) cc_final: 0.5706 (m-80) REVERT: V 9 MET cc_start: 0.3679 (ttp) cc_final: 0.3234 (tmm) REVERT: W 38 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.5890 (m90) REVERT: W 42 TYR cc_start: 0.5803 (t80) cc_final: 0.5583 (t80) REVERT: 1 9 MET cc_start: 0.4280 (mtt) cc_final: 0.3856 (mmm) REVERT: 1 27 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6905 (mm) REVERT: 2 27 LEU cc_start: 0.6343 (tt) cc_final: 0.5911 (tt) REVERT: 3 6 LYS cc_start: 0.6522 (mtpt) cc_final: 0.5796 (tttt) REVERT: 5 15 ARG cc_start: 0.5009 (ptp-110) cc_final: 0.4628 (ttp80) REVERT: 8 24 MET cc_start: 0.5026 (mmm) cc_final: 0.4626 (mmp) REVERT: U 13 MET cc_start: 0.5187 (mmm) cc_final: 0.4905 (mmm) REVERT: l 72 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6960 (pp20) REVERT: i 35 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8004 (mp) REVERT: v 17 PHE cc_start: 0.7309 (m-80) cc_final: 0.6988 (t80) REVERT: z 19 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6403 (tp) REVERT: z 39 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7753 (tp) REVERT: 01 8 TRP cc_start: 0.7552 (m100) cc_final: 0.7240 (m100) REVERT: 05 24 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7052 (tt) REVERT: 06 24 MET cc_start: 0.6701 (mmm) cc_final: 0.6185 (ptp) outliers start: 188 outliers final: 92 residues processed: 885 average time/residue: 0.9273 time to fit residues: 1091.7460 Evaluate side-chains 835 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 730 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain T residue 38 HIS Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 2 residue 38 HIS Chi-restraints excluded: chain 3 residue 36 LEU Chi-restraints excluded: chain 3 residue 40 SER Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain 4 residue 48 PHE Chi-restraints excluded: chain 6 residue 36 VAL Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 57 ILE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 137 VAL Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain h residue 175 MET Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 11 LEU Chi-restraints excluded: chain b residue 14 GLU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain j residue 17 GLN Chi-restraints excluded: chain k residue 10 ILE Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 43 ILE Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 27 LEU Chi-restraints excluded: chain s residue 40 SER Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain t residue 12 THR Chi-restraints excluded: chain t residue 41 VAL Chi-restraints excluded: chain v residue 37 SER Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 24 LEU Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 19 LEU Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain z residue 31 SER Chi-restraints excluded: chain z residue 39 LEU Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain 02 residue 39 LEU Chi-restraints excluded: chain 03 residue 29 VAL Chi-restraints excluded: chain 03 residue 30 MET Chi-restraints excluded: chain 03 residue 37 SER Chi-restraints excluded: chain 03 residue 54 VAL Chi-restraints excluded: chain 04 residue 21 SER Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain 05 residue 18 VAL Chi-restraints excluded: chain 05 residue 24 LEU Chi-restraints excluded: chain 06 residue 31 SER Chi-restraints excluded: chain x residue 42 LEU Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 5.9990 chunk 293 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 chunk 262 optimal weight: 0.6980 chunk 391 optimal weight: 0.9980 chunk 414 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 chunk 371 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 HIS h 206 ASN a 20 GLN ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN q 20 GLN v 20 GLN 01 20 GLN 01 42 ASN ** 07 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 47992 Z= 0.184 Angle : 0.713 14.499 65615 Z= 0.286 Chirality : 0.038 0.241 6467 Planarity : 0.004 0.057 7851 Dihedral : 18.434 179.839 10758 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.28 % Allowed : 17.96 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.12), residues: 4376 helix: 2.25 (0.09), residues: 2874 sheet: -0.35 (0.76), residues: 46 loop : -0.23 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP g 44 HIS 0.014 0.001 HIS z 20 PHE 0.029 0.001 PHE L 216 TYR 0.018 0.001 TYR t 23 ARG 0.006 0.000 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 782 time to evaluate : 3.320 Fit side-chains revert: symmetry clash REVERT: L 243 PHE cc_start: 0.7431 (m-10) cc_final: 0.7130 (m-10) REVERT: M 138 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6448 (tp40) REVERT: E 6 LEU cc_start: 0.5530 (OUTLIER) cc_final: 0.5248 (pp) REVERT: N 18 GLU cc_start: 0.7093 (tp30) cc_final: 0.6867 (tp30) REVERT: Q 20 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6747 (tp40) REVERT: S 9 MET cc_start: 0.4279 (mtp) cc_final: 0.3837 (mtp) REVERT: S 15 ARG cc_start: 0.5145 (tmm160) cc_final: 0.3983 (ttt180) REVERT: T 19 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7748 (tt) REVERT: V 4 PHE cc_start: 0.6011 (m-80) cc_final: 0.5719 (m-80) REVERT: V 9 MET cc_start: 0.3595 (ttp) cc_final: 0.3060 (tmm) REVERT: W 38 HIS cc_start: 0.6754 (OUTLIER) cc_final: 0.6019 (m90) REVERT: 1 9 MET cc_start: 0.4057 (mtt) cc_final: 0.3660 (mmm) REVERT: 1 27 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6810 (mm) REVERT: 1 31 ILE cc_start: 0.7778 (mp) cc_final: 0.7352 (mt) REVERT: 2 27 LEU cc_start: 0.6321 (tt) cc_final: 0.5898 (tt) REVERT: 3 6 LYS cc_start: 0.6491 (mtpt) cc_final: 0.5880 (tttt) REVERT: 5 15 ARG cc_start: 0.5014 (ptp-110) cc_final: 0.4622 (ttp80) REVERT: 7 45 GLU cc_start: 0.5236 (mm-30) cc_final: 0.4747 (tp30) REVERT: 8 24 MET cc_start: 0.4879 (mmm) cc_final: 0.4479 (mmt) REVERT: U 13 MET cc_start: 0.4987 (mmm) cc_final: 0.4724 (mmm) REVERT: l 72 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6941 (pp20) REVERT: m 263 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: g 36 VAL cc_start: 0.7340 (OUTLIER) cc_final: 0.7004 (t) REVERT: i 35 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7929 (mp) REVERT: n 42 TYR cc_start: 0.8007 (t80) cc_final: 0.7792 (t80) REVERT: v 17 PHE cc_start: 0.7287 (m-80) cc_final: 0.7007 (t80) REVERT: z 19 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6371 (tp) REVERT: z 39 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7669 (tp) REVERT: 01 8 TRP cc_start: 0.7401 (m100) cc_final: 0.7038 (m100) REVERT: 01 9 MET cc_start: 0.6735 (OUTLIER) cc_final: 0.6473 (mtm) REVERT: 06 24 MET cc_start: 0.6663 (mmm) cc_final: 0.6133 (ptp) outliers start: 159 outliers final: 59 residues processed: 868 average time/residue: 0.9606 time to fit residues: 1106.4878 Evaluate side-chains 797 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 725 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 38 HIS Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain Y residue 11 PHE Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 2 residue 38 HIS Chi-restraints excluded: chain 4 residue 9 THR Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 48 PHE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 263 GLU Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 175 MET Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 11 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain j residue 17 GLN Chi-restraints excluded: chain j residue 39 LEU Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain t residue 12 THR Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 19 LEU Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain z residue 31 SER Chi-restraints excluded: chain z residue 39 LEU Chi-restraints excluded: chain 01 residue 9 MET Chi-restraints excluded: chain 03 residue 37 SER Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 308 optimal weight: 0.7980 chunk 171 optimal weight: 0.5980 chunk 353 optimal weight: 7.9990 chunk 286 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 211 optimal weight: 0.6980 chunk 372 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN R 20 HIS T 15 GLN ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN h 206 ASN a 20 GLN ** g 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN q 20 GLN ** v 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 52 ASN 01 42 ASN ** 07 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 47992 Z= 0.233 Angle : 0.738 15.439 65615 Z= 0.299 Chirality : 0.040 0.244 6467 Planarity : 0.004 0.060 7851 Dihedral : 18.129 179.837 10755 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.85 % Allowed : 18.04 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.12), residues: 4376 helix: 2.20 (0.09), residues: 2880 sheet: -0.39 (0.76), residues: 46 loop : -0.26 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP g 44 HIS 0.014 0.001 HIS z 20 PHE 0.027 0.001 PHE L 216 TYR 0.022 0.002 TYR y 5 ARG 0.005 0.000 ARG j 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 770 time to evaluate : 3.356 Fit side-chains revert: symmetry clash REVERT: L 243 PHE cc_start: 0.7456 (m-10) cc_final: 0.7148 (m-10) REVERT: M 138 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6514 (tp40) REVERT: M 263 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7912 (tm-30) REVERT: H 177 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7024 (mmp-170) REVERT: E 6 LEU cc_start: 0.5585 (OUTLIER) cc_final: 0.5264 (pp) REVERT: G 14 GLU cc_start: 0.6834 (mp0) cc_final: 0.6496 (mp0) REVERT: N 13 ASP cc_start: 0.6791 (m-30) cc_final: 0.6582 (m-30) REVERT: Q 20 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6786 (tp40) REVERT: S 15 ARG cc_start: 0.5116 (tmm160) cc_final: 0.3956 (ttt180) REVERT: T 19 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7710 (tt) REVERT: V 4 PHE cc_start: 0.6014 (m-80) cc_final: 0.5698 (m-80) REVERT: V 9 MET cc_start: 0.3658 (ttp) cc_final: 0.3136 (tmm) REVERT: W 38 HIS cc_start: 0.6614 (OUTLIER) cc_final: 0.5711 (m90) REVERT: 1 9 MET cc_start: 0.4022 (mtt) cc_final: 0.3596 (mmm) REVERT: 1 27 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6889 (mm) REVERT: 1 31 ILE cc_start: 0.7813 (mp) cc_final: 0.7410 (mt) REVERT: 2 27 LEU cc_start: 0.6298 (tt) cc_final: 0.5887 (tt) REVERT: 3 6 LYS cc_start: 0.6433 (mtpt) cc_final: 0.5811 (tttt) REVERT: 5 15 ARG cc_start: 0.5133 (ptp-110) cc_final: 0.4694 (ttp80) REVERT: 7 45 GLU cc_start: 0.5129 (mm-30) cc_final: 0.4669 (tp30) REVERT: 8 24 MET cc_start: 0.4964 (mmm) cc_final: 0.4502 (mmt) REVERT: U 13 MET cc_start: 0.5019 (mmm) cc_final: 0.4759 (mmm) REVERT: l 72 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6923 (pp20) REVERT: m 263 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: g 17 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: g 36 VAL cc_start: 0.7338 (OUTLIER) cc_final: 0.7008 (t) REVERT: i 35 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7962 (mp) REVERT: v 17 PHE cc_start: 0.7272 (m-80) cc_final: 0.6970 (t80) REVERT: z 39 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7718 (tp) REVERT: 01 8 TRP cc_start: 0.7411 (m100) cc_final: 0.7038 (m100) REVERT: 06 24 MET cc_start: 0.6632 (mmm) cc_final: 0.6104 (ptp) REVERT: 07 9 MET cc_start: 0.1265 (OUTLIER) cc_final: 0.0770 (mmt) outliers start: 180 outliers final: 73 residues processed: 861 average time/residue: 0.9598 time to fit residues: 1106.8900 Evaluate side-chains 812 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 724 time to evaluate : 3.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 20 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain T residue 38 HIS Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain Y residue 11 PHE Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 2 residue 38 HIS Chi-restraints excluded: chain 4 residue 9 THR Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 48 PHE Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 137 VAL Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 263 GLU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 11 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain e residue 35 ILE Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 38 THR Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 17 GLN Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain j residue 17 GLN Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain j residue 39 LEU Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain z residue 31 SER Chi-restraints excluded: chain z residue 39 LEU Chi-restraints excluded: chain 02 residue 39 LEU Chi-restraints excluded: chain 03 residue 27 LEU Chi-restraints excluded: chain 03 residue 30 MET Chi-restraints excluded: chain 03 residue 37 SER Chi-restraints excluded: chain 03 residue 54 VAL Chi-restraints excluded: chain 04 residue 21 SER Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain 07 residue 9 MET Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 10.0000 chunk 373 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 243 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 chunk 415 optimal weight: 1.9990 chunk 344 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 44 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 56 GLN ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 206 ASN a 20 GLN ** g 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN y 52 ASN 01 42 ASN ** 07 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 47992 Z= 0.206 Angle : 0.719 15.234 65615 Z= 0.293 Chirality : 0.039 0.251 6467 Planarity : 0.004 0.064 7851 Dihedral : 17.759 179.845 10752 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.51 % Favored : 97.46 % Rotamer: Outliers : 4.07 % Allowed : 19.07 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.12), residues: 4376 helix: 2.15 (0.09), residues: 2956 sheet: -0.57 (0.73), residues: 48 loop : -0.01 (0.18), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP g 44 HIS 0.014 0.001 HIS z 20 PHE 0.027 0.001 PHE L 216 TYR 0.030 0.001 TYR F 5 ARG 0.004 0.000 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 771 time to evaluate : 3.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 205 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6909 (pt0) REVERT: L 243 PHE cc_start: 0.7452 (m-10) cc_final: 0.7172 (m-10) REVERT: M 138 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6425 (tp40) REVERT: M 263 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: E 6 LEU cc_start: 0.5635 (OUTLIER) cc_final: 0.5352 (pp) REVERT: G 14 GLU cc_start: 0.6802 (mp0) cc_final: 0.6454 (mp0) REVERT: N 13 ASP cc_start: 0.6769 (m-30) cc_final: 0.6568 (m-30) REVERT: Q 20 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6766 (tp40) REVERT: S 9 MET cc_start: 0.4448 (OUTLIER) cc_final: 0.3698 (mtp) REVERT: S 15 ARG cc_start: 0.5140 (tmm160) cc_final: 0.3983 (ttt180) REVERT: T 19 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7688 (tt) REVERT: V 4 PHE cc_start: 0.6021 (m-80) cc_final: 0.5716 (m-80) REVERT: V 9 MET cc_start: 0.3693 (ttp) cc_final: 0.3089 (tmm) REVERT: W 38 HIS cc_start: 0.6645 (OUTLIER) cc_final: 0.5731 (m90) REVERT: 1 9 MET cc_start: 0.4008 (mtt) cc_final: 0.3643 (mmm) REVERT: 1 27 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6853 (mm) REVERT: 1 31 ILE cc_start: 0.7816 (mp) cc_final: 0.7427 (mt) REVERT: 2 27 LEU cc_start: 0.6283 (tt) cc_final: 0.5864 (tt) REVERT: 3 6 LYS cc_start: 0.6449 (mtpt) cc_final: 0.5797 (tttt) REVERT: 7 45 GLU cc_start: 0.5106 (mm-30) cc_final: 0.4670 (tp30) REVERT: 8 24 MET cc_start: 0.4962 (mmm) cc_final: 0.4500 (mmt) REVERT: X 20 ARG cc_start: 0.6601 (mtm180) cc_final: 0.6197 (mtt90) REVERT: U 13 MET cc_start: 0.4999 (mmm) cc_final: 0.4723 (mmm) REVERT: l 72 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6903 (pp20) REVERT: m 263 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: g 17 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: g 36 VAL cc_start: 0.7387 (OUTLIER) cc_final: 0.7048 (t) REVERT: i 35 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7982 (mp) REVERT: v 17 PHE cc_start: 0.7300 (m-80) cc_final: 0.6994 (t80) REVERT: z 39 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7710 (tp) REVERT: 01 8 TRP cc_start: 0.7430 (m100) cc_final: 0.7145 (m100) REVERT: 05 24 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7056 (tt) REVERT: 06 24 MET cc_start: 0.6661 (mmm) cc_final: 0.6133 (ptp) outliers start: 151 outliers final: 66 residues processed: 852 average time/residue: 0.9453 time to fit residues: 1071.5868 Evaluate side-chains 813 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 731 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 9 MET Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 38 HIS Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain Y residue 37 SER Chi-restraints excluded: chain Z residue 18 GLU Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 2 residue 38 HIS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 48 PHE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 137 VAL Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 263 GLU Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain e residue 35 ILE Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 38 THR Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 17 GLN Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain j residue 17 GLN Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain j residue 39 LEU Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 40 SER Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain z residue 31 SER Chi-restraints excluded: chain z residue 39 LEU Chi-restraints excluded: chain 02 residue 39 LEU Chi-restraints excluded: chain 03 residue 27 LEU Chi-restraints excluded: chain 03 residue 30 MET Chi-restraints excluded: chain 03 residue 54 VAL Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain 05 residue 24 LEU Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 236 optimal weight: 4.9990 chunk 303 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 349 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 413 optimal weight: 20.0000 chunk 258 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 44 ASN H 129 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 GLN ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN l 56 GLN ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 81 ASN h 206 ASN a 20 GLN ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN q 20 GLN ** r 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 52 ASN 01 42 ASN ** 07 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 47992 Z= 0.495 Angle : 0.945 19.787 65615 Z= 0.383 Chirality : 0.048 0.370 6467 Planarity : 0.005 0.068 7851 Dihedral : 19.353 179.944 10750 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 5.12 % Allowed : 19.10 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.12), residues: 4376 helix: 1.53 (0.09), residues: 2946 sheet: -0.80 (0.71), residues: 46 loop : -0.28 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP y 8 HIS 0.017 0.002 HIS E 38 PHE 0.035 0.003 PHE L 216 TYR 0.024 0.003 TYR I 51 ARG 0.007 0.001 ARG M 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 746 time to evaluate : 3.283 Fit side-chains revert: symmetry clash REVERT: L 2 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8699 (mt) REVERT: M 138 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6629 (tp40) REVERT: M 214 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8964 (tt) REVERT: M 263 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: H 248 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6318 (mmm-85) REVERT: E 6 LEU cc_start: 0.5542 (OUTLIER) cc_final: 0.5243 (pp) REVERT: Q 20 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6895 (tp40) REVERT: S 9 MET cc_start: 0.4467 (OUTLIER) cc_final: 0.3703 (mtp) REVERT: S 15 ARG cc_start: 0.5322 (tmm160) cc_final: 0.4086 (ttt180) REVERT: T 19 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7586 (tt) REVERT: V 4 PHE cc_start: 0.6005 (m-80) cc_final: 0.5696 (m-80) REVERT: V 9 MET cc_start: 0.3466 (ttp) cc_final: 0.2952 (tmm) REVERT: W 38 HIS cc_start: 0.6748 (OUTLIER) cc_final: 0.5756 (m90) REVERT: W 42 TYR cc_start: 0.5401 (t80) cc_final: 0.5093 (t80) REVERT: 1 27 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6905 (mm) REVERT: 2 27 LEU cc_start: 0.6428 (tt) cc_final: 0.6026 (tt) REVERT: 8 24 MET cc_start: 0.5175 (mmm) cc_final: 0.4742 (mmp) REVERT: U 13 MET cc_start: 0.5174 (mmm) cc_final: 0.4917 (mmm) REVERT: l 72 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6893 (pp20) REVERT: m 263 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: i 35 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8165 (mp) REVERT: v 17 PHE cc_start: 0.7319 (m-80) cc_final: 0.6907 (t80) REVERT: 01 8 TRP cc_start: 0.7520 (m100) cc_final: 0.7261 (m100) REVERT: 05 24 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7209 (tt) REVERT: 06 24 MET cc_start: 0.6775 (mmm) cc_final: 0.6167 (ptp) outliers start: 190 outliers final: 88 residues processed: 847 average time/residue: 0.9477 time to fit residues: 1069.5514 Evaluate side-chains 821 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 718 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 248 ARG Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 9 MET Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain T residue 38 HIS Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain Y residue 36 LEU Chi-restraints excluded: chain Y residue 37 SER Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 36 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 2 residue 38 HIS Chi-restraints excluded: chain 4 residue 9 THR Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 48 PHE Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 57 ILE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 137 VAL Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 263 GLU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 11 LEU Chi-restraints excluded: chain b residue 14 GLU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 38 THR Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 17 GLN Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain q residue 44 LEU Chi-restraints excluded: chain r residue 6 LEU Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 40 SER Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain t residue 12 THR Chi-restraints excluded: chain t residue 41 VAL Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain z residue 31 SER Chi-restraints excluded: chain z residue 39 LEU Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain 02 residue 39 LEU Chi-restraints excluded: chain 03 residue 30 MET Chi-restraints excluded: chain 03 residue 40 SER Chi-restraints excluded: chain 03 residue 54 VAL Chi-restraints excluded: chain 04 residue 21 SER Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain 05 residue 7 ILE Chi-restraints excluded: chain 05 residue 24 LEU Chi-restraints excluded: chain 07 residue 22 VAL Chi-restraints excluded: chain x residue 42 LEU Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 80 optimal weight: 0.3980 chunk 262 optimal weight: 0.6980 chunk 281 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 325 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 129 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 56 GLN m 4 GLN h 206 ASN a 20 GLN i 20 GLN ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 15 GLN y 52 ASN 01 42 ASN ** 07 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 47992 Z= 0.179 Angle : 0.722 14.619 65615 Z= 0.297 Chirality : 0.039 0.254 6467 Planarity : 0.003 0.050 7851 Dihedral : 17.894 179.873 10748 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.26 % Favored : 97.71 % Rotamer: Outliers : 3.15 % Allowed : 21.60 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.12), residues: 4376 helix: 2.02 (0.09), residues: 2950 sheet: -0.70 (0.73), residues: 48 loop : -0.09 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP06 44 HIS 0.011 0.001 HIS z 20 PHE 0.031 0.001 PHE x 38 TYR 0.021 0.001 TYR F 5 ARG 0.007 0.000 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 770 time to evaluate : 6.400 Fit side-chains revert: symmetry clash REVERT: L 243 PHE cc_start: 0.7422 (m-10) cc_final: 0.7124 (m-10) REVERT: M 2 GLU cc_start: 0.5918 (mp0) cc_final: 0.5609 (mp0) REVERT: M 138 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6429 (tp40) REVERT: E 6 LEU cc_start: 0.5557 (OUTLIER) cc_final: 0.5279 (pp) REVERT: G 14 GLU cc_start: 0.6718 (mp0) cc_final: 0.6338 (mp0) REVERT: Q 9 MET cc_start: 0.5715 (mpp) cc_final: 0.5413 (mmm) REVERT: S 9 MET cc_start: 0.4461 (OUTLIER) cc_final: 0.3747 (mtp) REVERT: S 15 ARG cc_start: 0.5104 (tmm160) cc_final: 0.4135 (ttm-80) REVERT: S 45 GLU cc_start: 0.7332 (pt0) cc_final: 0.7094 (pt0) REVERT: T 19 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7673 (tt) REVERT: V 4 PHE cc_start: 0.6072 (m-80) cc_final: 0.5810 (m-80) REVERT: V 9 MET cc_start: 0.3499 (ttp) cc_final: 0.2915 (tmm) REVERT: W 38 HIS cc_start: 0.6600 (OUTLIER) cc_final: 0.5727 (m90) REVERT: 1 27 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6797 (mm) REVERT: 1 31 ILE cc_start: 0.7827 (mp) cc_final: 0.7402 (mt) REVERT: 3 6 LYS cc_start: 0.6616 (mtpt) cc_final: 0.5989 (tttt) REVERT: 3 9 MET cc_start: 0.3086 (tpp) cc_final: 0.2858 (tpp) REVERT: 3 29 VAL cc_start: 0.7951 (m) cc_final: 0.7728 (t) REVERT: 4 43 ILE cc_start: 0.6681 (mp) cc_final: 0.6199 (tp) REVERT: 7 45 GLU cc_start: 0.5167 (mm-30) cc_final: 0.4728 (tp30) REVERT: 8 24 MET cc_start: 0.5016 (mmm) cc_final: 0.4383 (mmt) REVERT: X 20 ARG cc_start: 0.6584 (mtm180) cc_final: 0.6186 (mtt90) REVERT: U 13 MET cc_start: 0.4983 (mmm) cc_final: 0.4764 (mmm) REVERT: l 72 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6888 (pp20) REVERT: m 263 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: g 36 VAL cc_start: 0.7372 (OUTLIER) cc_final: 0.7011 (t) REVERT: v 17 PHE cc_start: 0.7295 (m-80) cc_final: 0.6976 (t80) REVERT: y 5 TYR cc_start: 0.6761 (p90) cc_final: 0.6521 (p90) REVERT: 06 24 MET cc_start: 0.6653 (mmm) cc_final: 0.6149 (ptp) REVERT: 06 44 TRP cc_start: 0.7051 (t60) cc_final: 0.6807 (t60) REVERT: 07 44 LEU cc_start: 0.7403 (mt) cc_final: 0.7013 (mp) outliers start: 117 outliers final: 52 residues processed: 834 average time/residue: 1.0509 time to fit residues: 1189.1663 Evaluate side-chains 790 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 729 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain S residue 9 MET Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain T residue 38 HIS Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain Y residue 37 SER Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 2 residue 38 HIS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 48 PHE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 137 VAL Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 263 GLU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 40 SER Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain z residue 31 SER Chi-restraints excluded: chain 03 residue 3 LYS Chi-restraints excluded: chain 03 residue 54 VAL Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 10.0000 chunk 396 optimal weight: 2.9990 chunk 361 optimal weight: 2.9990 chunk 385 optimal weight: 8.9990 chunk 231 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 chunk 302 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 348 optimal weight: 5.9990 chunk 364 optimal weight: 7.9990 chunk 383 optimal weight: 0.0670 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 44 ASN H 32 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 15 GLN ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN a 20 GLN ** g 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN y 52 ASN z 17 GLN 01 42 ASN ** 07 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 47992 Z= 0.294 Angle : 0.795 15.846 65615 Z= 0.327 Chirality : 0.042 0.302 6467 Planarity : 0.004 0.101 7851 Dihedral : 18.233 179.888 10748 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.11 % Favored : 96.87 % Rotamer: Outliers : 3.12 % Allowed : 22.08 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.12), residues: 4376 helix: 1.88 (0.09), residues: 2956 sheet: -0.81 (0.70), residues: 48 loop : -0.16 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 41 HIS 0.012 0.002 HIS z 20 PHE 0.033 0.002 PHE L 216 TYR 0.021 0.002 TYR o 5 ARG 0.006 0.001 ARG M 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 735 time to evaluate : 3.342 Fit side-chains revert: symmetry clash REVERT: L 243 PHE cc_start: 0.7475 (m-10) cc_final: 0.7141 (m-10) REVERT: M 2 GLU cc_start: 0.5896 (mp0) cc_final: 0.5606 (mp0) REVERT: M 138 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6506 (tp40) REVERT: M 306 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7967 (mm) REVERT: E 6 LEU cc_start: 0.5619 (OUTLIER) cc_final: 0.5346 (pp) REVERT: G 14 GLU cc_start: 0.6734 (mp0) cc_final: 0.6362 (mp0) REVERT: S 9 MET cc_start: 0.4461 (OUTLIER) cc_final: 0.3746 (mtp) REVERT: S 15 ARG cc_start: 0.5157 (tmm160) cc_final: 0.4005 (ttt180) REVERT: T 19 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7707 (tt) REVERT: V 4 PHE cc_start: 0.6079 (m-80) cc_final: 0.5817 (m-80) REVERT: V 9 MET cc_start: 0.3455 (ttp) cc_final: 0.2874 (tmm) REVERT: W 38 HIS cc_start: 0.6668 (OUTLIER) cc_final: 0.5767 (m90) REVERT: Y 18 VAL cc_start: 0.7740 (p) cc_final: 0.7484 (m) REVERT: 1 27 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6829 (mm) REVERT: 1 31 ILE cc_start: 0.7856 (mp) cc_final: 0.7421 (mt) REVERT: 2 27 LEU cc_start: 0.6313 (tt) cc_final: 0.5876 (tt) REVERT: 3 29 VAL cc_start: 0.7947 (m) cc_final: 0.7715 (t) REVERT: 4 42 TYR cc_start: 0.5028 (OUTLIER) cc_final: 0.4450 (t80) REVERT: 4 43 ILE cc_start: 0.6799 (mp) cc_final: 0.6401 (tp) REVERT: 8 24 MET cc_start: 0.5226 (mmm) cc_final: 0.4591 (mmt) REVERT: U 13 MET cc_start: 0.4999 (mmm) cc_final: 0.4744 (mmm) REVERT: l 72 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6927 (pp20) REVERT: m 263 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: h 173 GLU cc_start: 0.6662 (tp30) cc_final: 0.6290 (tp30) REVERT: r 15 GLN cc_start: 0.6752 (pm20) cc_final: 0.6490 (pm20) REVERT: v 17 PHE cc_start: 0.7331 (m-80) cc_final: 0.6933 (t80) REVERT: y 5 TYR cc_start: 0.6814 (p90) cc_final: 0.6573 (p90) REVERT: 01 8 TRP cc_start: 0.7356 (m100) cc_final: 0.7016 (m100) REVERT: 06 24 MET cc_start: 0.6712 (mmm) cc_final: 0.6160 (ptp) REVERT: 07 30 MET cc_start: 0.5185 (tpt) cc_final: 0.4909 (tpp) outliers start: 116 outliers final: 71 residues processed: 806 average time/residue: 0.9759 time to fit residues: 1041.3428 Evaluate side-chains 798 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 717 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain M residue 306 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain S residue 9 MET Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain T residue 38 HIS Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain Y residue 37 SER Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 2 residue 38 HIS Chi-restraints excluded: chain 4 residue 6 LEU Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain 4 residue 42 TYR Chi-restraints excluded: chain 4 residue 48 PHE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 137 VAL Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 263 GLU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 14 GLU Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 38 THR Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 40 SER Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain t residue 12 THR Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain z residue 31 SER Chi-restraints excluded: chain 02 residue 39 LEU Chi-restraints excluded: chain 03 residue 54 VAL Chi-restraints excluded: chain 04 residue 21 SER Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain 05 residue 10 ILE Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 0.0870 chunk 407 optimal weight: 0.5980 chunk 248 optimal weight: 7.9990 chunk 193 optimal weight: 2.9990 chunk 283 optimal weight: 0.7980 chunk 427 optimal weight: 1.9990 chunk 393 optimal weight: 2.9990 chunk 340 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 44 ASN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN i 20 GLN ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 52 ASN 01 42 ASN ** 07 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 47992 Z= 0.179 Angle : 0.718 14.704 65615 Z= 0.298 Chirality : 0.039 0.271 6467 Planarity : 0.004 0.079 7851 Dihedral : 17.499 179.862 10748 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.35 % Favored : 97.62 % Rotamer: Outliers : 2.21 % Allowed : 23.11 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.12), residues: 4376 helix: 2.07 (0.09), residues: 2956 sheet: -0.71 (0.71), residues: 48 loop : -0.08 (0.18), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 44 HIS 0.010 0.001 HIS z 20 PHE 0.035 0.001 PHE x 38 TYR 0.020 0.001 TYR F 5 ARG 0.008 0.000 ARG M 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 771 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 2 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8634 (mt) REVERT: L 243 PHE cc_start: 0.7411 (m-10) cc_final: 0.7143 (m-10) REVERT: M 2 GLU cc_start: 0.5857 (mp0) cc_final: 0.5593 (mp0) REVERT: M 138 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6437 (tp40) REVERT: M 272 MET cc_start: 0.8793 (tpp) cc_final: 0.8499 (tpp) REVERT: E 6 LEU cc_start: 0.5416 (OUTLIER) cc_final: 0.5178 (pp) REVERT: G 14 GLU cc_start: 0.6637 (mp0) cc_final: 0.6283 (mp0) REVERT: S 9 MET cc_start: 0.4445 (OUTLIER) cc_final: 0.4146 (mtp) REVERT: S 15 ARG cc_start: 0.5054 (tmm160) cc_final: 0.4086 (ttm-80) REVERT: T 19 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7642 (tt) REVERT: V 4 PHE cc_start: 0.6089 (m-80) cc_final: 0.5847 (m-80) REVERT: V 9 MET cc_start: 0.3534 (ttp) cc_final: 0.2909 (tmm) REVERT: W 38 HIS cc_start: 0.6599 (OUTLIER) cc_final: 0.5880 (m90) REVERT: Y 25 PHE cc_start: 0.7609 (t80) cc_final: 0.7315 (t80) REVERT: 1 27 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6841 (mm) REVERT: 1 31 ILE cc_start: 0.7804 (mp) cc_final: 0.7407 (mt) REVERT: 2 27 LEU cc_start: 0.6306 (tt) cc_final: 0.5893 (tt) REVERT: 3 29 VAL cc_start: 0.7899 (m) cc_final: 0.7694 (t) REVERT: 4 43 ILE cc_start: 0.6709 (mp) cc_final: 0.6310 (tp) REVERT: 7 45 GLU cc_start: 0.5091 (mm-30) cc_final: 0.4680 (tp30) REVERT: 8 24 MET cc_start: 0.5004 (mmm) cc_final: 0.4365 (mmt) REVERT: X 20 ARG cc_start: 0.6630 (mtm180) cc_final: 0.6277 (mtt90) REVERT: U 13 MET cc_start: 0.4931 (mmm) cc_final: 0.4716 (mmm) REVERT: l 72 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6940 (pp20) REVERT: m 263 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: d 44 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.5941 (mm) REVERT: g 36 VAL cc_start: 0.7382 (OUTLIER) cc_final: 0.7008 (t) REVERT: v 17 PHE cc_start: 0.7270 (m-80) cc_final: 0.6945 (t80) REVERT: y 5 TYR cc_start: 0.6624 (p90) cc_final: 0.6384 (p90) REVERT: 01 8 TRP cc_start: 0.7342 (m100) cc_final: 0.6924 (m100) REVERT: 05 24 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7180 (tt) REVERT: 06 24 MET cc_start: 0.6599 (mmm) cc_final: 0.6174 (ptp) REVERT: 07 30 MET cc_start: 0.5107 (tpt) cc_final: 0.4497 (tpt) REVERT: 07 44 LEU cc_start: 0.7365 (mt) cc_final: 0.6979 (mp) outliers start: 82 outliers final: 50 residues processed: 821 average time/residue: 0.9657 time to fit residues: 1052.8380 Evaluate side-chains 789 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 727 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain S residue 9 MET Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain T residue 38 HIS Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain Y residue 37 SER Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 2 residue 38 HIS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain 4 residue 48 PHE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 263 GLU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 44 LEU Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 40 SER Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain 03 residue 54 VAL Chi-restraints excluded: chain 04 residue 21 SER Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain 05 residue 24 LEU Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 0.7980 chunk 362 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 313 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 340 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 350 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 44 ASN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN h 206 ASN a 20 GLN ** g 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 15 GLN t 20 HIS y 52 ASN 01 42 ASN ** 07 32 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 = 0.4140 r_free = 0.4140 target = 0.168370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.136627 restraints weight = 69838.410| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.30 r_work: 0.3404 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 47992 Z= 0.178 Angle : 0.708 14.563 65615 Z= 0.296 Chirality : 0.039 0.284 6467 Planarity : 0.003 0.075 7851 Dihedral : 17.087 179.863 10744 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.56 % Favored : 97.42 % Rotamer: Outliers : 1.99 % Allowed : 23.46 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.12), residues: 4376 helix: 2.11 (0.09), residues: 2958 sheet: -0.48 (0.74), residues: 46 loop : -0.08 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 44 HIS 0.017 0.001 HIS N 20 PHE 0.030 0.001 PHE 3 25 TYR 0.020 0.001 TYR t 23 ARG 0.007 0.000 ARG N 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16044.43 seconds wall clock time: 275 minutes 50.87 seconds (16550.87 seconds total)