Starting phenix.real_space_refine on Tue Nov 19 02:24:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpt_26063/11_2024/7tpt_26063.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpt_26063/11_2024/7tpt_26063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpt_26063/11_2024/7tpt_26063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpt_26063/11_2024/7tpt_26063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpt_26063/11_2024/7tpt_26063.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpt_26063/11_2024/7tpt_26063.cif" } resolution = 3.9 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= 0.002 sd= 0.033 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: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 16 5.21 5 S 263 5.16 5 C 31637 2.51 5 N 8979 2.21 5 O 9828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 50755 Number of models: 1 Model: "" Number of chains: 67 Chain: "A" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3310 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 26, 'TRANS': 387} Chain: "B" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3081 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 17, 'TRANS': 367} Chain: "C" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2744 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 14, 'TRANS': 348} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2287 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 9, 'TRANS': 273} Chain: "E" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1411 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 11, 'TRANS': 161} Chain: "F" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1379 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain: "G" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1002 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 1833 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 314} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1141 Unresolved non-hydrogen angles: 1464 Unresolved non-hydrogen dihedrals: 959 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 11, 'HIC:plan-2': 1, 'HIC:plan-1': 1, 'ASP:plan': 20, 'TYR:plan': 16, 'PHE%COO:plan': 1, 'ASN:plan1': 12, 'TRP:plan': 4, 'HIS:plan': 8, 'PHE:plan': 11, 'GLU:plan': 27, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 605 Chain: "K" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 1833 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 314} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1141 Unresolved non-hydrogen angles: 1464 Unresolved non-hydrogen dihedrals: 959 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 11, 'HIC:plan-2': 1, 'HIC:plan-1': 1, 'ASP:plan': 20, 'TYR:plan': 16, 'PHE%COO:plan': 1, 'ASN:plan1': 12, 'TRP:plan': 4, 'HIS:plan': 8, 'PHE:plan': 11, 'GLU:plan': 27, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 605 Chain: "L" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 1833 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 314} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1141 Unresolved non-hydrogen angles: 1464 Unresolved non-hydrogen dihedrals: 959 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 11, 'HIC:plan-2': 1, 'HIC:plan-1': 1, 'ASP:plan': 20, 'TYR:plan': 16, 'PHE%COO:plan': 1, 'ASN:plan1': 12, 'TRP:plan': 4, 'HIS:plan': 8, 'PHE:plan': 11, 'GLU:plan': 27, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 605 Chain: "M" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 1840 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 313} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1133 Unresolved non-hydrogen angles: 1453 Unresolved non-hydrogen dihedrals: 951 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 11, 'HIC:plan-2': 1, 'HIC:plan-1': 1, 'ASP:plan': 20, 'TYR:plan': 15, 'PHE%COO:plan': 1, 'ASN:plan1': 12, 'TRP:plan': 4, 'HIS:plan': 8, 'PHE:plan': 11, 'GLU:plan': 27, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 598 Chain: "N" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 1833 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 314} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1141 Unresolved non-hydrogen angles: 1464 Unresolved non-hydrogen dihedrals: 959 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 11, 'HIC:plan-2': 1, 'HIC:plan-1': 1, 'ASP:plan': 20, 'TYR:plan': 16, 'PHE%COO:plan': 1, 'ASN:plan1': 12, 'TRP:plan': 4, 'HIS:plan': 8, 'PHE:plan': 11, 'GLU:plan': 27, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 605 Chain: "U" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 1833 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 314} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1141 Unresolved non-hydrogen angles: 1464 Unresolved non-hydrogen dihedrals: 959 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 11, 'HIC:plan-2': 1, 'HIC:plan-1': 1, 'ASP:plan': 20, 'TYR:plan': 16, 'PHE%COO:plan': 1, 'ASN:plan1': 12, 'TRP:plan': 4, 'HIS:plan': 8, 'PHE:plan': 11, 'GLU:plan': 27, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 605 Chain: "a" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 33.35, per 1000 atoms: 0.66 Number of scatterers: 50755 At special positions: 0 Unit cell: (134.4, 323.68, 290.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 263 16.00 P 32 15.00 Mg 16 11.99 O 9828 8.00 N 8979 7.00 C 31637 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=0, symmetry=0 Links applied TRANS " TRP a 1 " - " ALA a 7 " " DTH a 4 " - " ALA a 3 " " TRP b 1 " - " ALA b 7 " " DTH b 4 " - " ALA b 3 " " TRP c 1 " - " ALA c 7 " " DTH c 4 " - " ALA c 3 " " TRP d 1 " - " ALA d 7 " " DTH d 4 " - " ALA d 3 " " TRP e 1 " - " ALA e 7 " " DTH e 4 " - " ALA e 3 " " TRP f 1 " - " ALA f 7 " " DTH f 4 " - " ALA f 3 " " TRP g 1 " - " ALA g 7 " " DTH g 4 " - " ALA g 3 " " TRP h 1 " - " ALA h 7 " " DTH h 4 " - " ALA h 3 " " TRP i 1 " - " ALA i 7 " " DTH i 4 " - " ALA i 3 " " TRP j 1 " - " ALA j 7 " " DTH j 4 " - " ALA j 3 " " TRP k 1 " - " ALA k 7 " " DTH k 4 " - " ALA k 3 " " TRP l 1 " - " ALA l 7 " " DTH l 4 " - " ALA l 3 " " TRP m 1 " - " ALA m 7 " " DTH m 4 " - " ALA m 3 " " TRP n 1 " - " ALA n 7 " " DTH n 4 " - " ALA n 3 " " TRP o 1 " - " ALA o 7 " " DTH o 4 " - " ALA o 3 " Time building additional restraints: 13.28 Conformation dependent library (CDL) restraints added in 7.2 seconds 14082 Ramachandran restraints generated. 7041 Oldfield, 0 Emsley, 7041 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH a 4 " pdb=" CB DTH b 4 " pdb=" CB DTH c 4 " pdb=" CB DTH d 4 " pdb=" CB DTH e 4 " pdb=" CB DTH f 4 " pdb=" CB DTH g 4 " pdb=" CB DTH h 4 " pdb=" CB DTH i 4 " pdb=" CB DTH j 4 " pdb=" CB DTH k 4 " pdb=" CB DTH l 4 " pdb=" CB DTH m 4 " pdb=" CB DTH n 4 " pdb=" CB DTH o 4 " Number of C-beta restraints generated: 13410 Finding SS restraints... Secondary structure from input PDB file: 349 helices and 106 sheets defined 47.1% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.44 Creating SS restraints... Processing helix chain 'A' and resid 53 through 59 removed outlier: 4.254A pdb=" N ASP A 57 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 removed outlier: 4.001A pdb=" N GLU A 65 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 104 through 107 Processing helix chain 'A' and resid 119 through 134 removed outlier: 3.619A pdb=" N ARG A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 153 removed outlier: 4.518A pdb=" N LEU A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.918A pdb=" N ASP A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 238 through 248 Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.989A pdb=" N GLY A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 282 through 283 No H-bonds generated for 'chain 'A' and resid 282 through 283' Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 308 through 318 removed outlier: 4.171A pdb=" N ARG A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Proline residue: A 314 - end of helix removed outlier: 3.894A pdb=" N LYS A 317 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN A 318 " --> pdb=" O PRO A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 4.101A pdb=" N PHE A 328 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 354 removed outlier: 3.560A pdb=" N LEU A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 387 Processing helix chain 'A' and resid 387 through 394 removed outlier: 4.054A pdb=" N TYR A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.520A pdb=" N TYR A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.992A pdb=" N ILE A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS A 410 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 65 removed outlier: 3.995A pdb=" N SER B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.506A pdb=" N CYS B 105 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 130 removed outlier: 4.121A pdb=" N ARG B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 176 through 179 removed outlier: 3.540A pdb=" N THR B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 179' Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.871A pdb=" N ARG B 214 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N MET B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 256 through 261 removed outlier: 3.776A pdb=" N GLU B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 261' Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 277 through 289 removed outlier: 3.528A pdb=" N ALA B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 4.219A pdb=" N SER B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 312 through 329 Processing helix chain 'B' and resid 334 through 338 removed outlier: 3.605A pdb=" N SER B 338 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 365 removed outlier: 3.642A pdb=" N ILE B 364 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 removed outlier: 4.131A pdb=" N GLN B 379 " --> pdb=" O ARG B 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 375 through 379' Processing helix chain 'C' and resid 297 through 308 removed outlier: 3.771A pdb=" N PHE C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 306 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS C 307 " --> pdb=" O GLN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.866A pdb=" N GLY C 320 " --> pdb=" O ALA C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 20 removed outlier: 3.667A pdb=" N GLU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 63 through 71 removed outlier: 3.635A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 115 removed outlier: 3.755A pdb=" N VAL D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET D 115 " --> pdb=" O HIS D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 135 removed outlier: 4.139A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 184 removed outlier: 3.523A pdb=" N VAL D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL D 176 " --> pdb=" O ASP D 172 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 210 removed outlier: 3.555A pdb=" N LYS D 210 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 236 through 246 removed outlier: 3.817A pdb=" N THR D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 278 removed outlier: 3.739A pdb=" N SER D 271 " --> pdb=" O ARG D 267 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP D 272 " --> pdb=" O ALA D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'E' and resid 40 through 53 removed outlier: 4.374A pdb=" N LYS E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ALA E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 83 removed outlier: 3.835A pdb=" N THR E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 100 Processing helix chain 'E' and resid 122 through 149 removed outlier: 3.868A pdb=" N ASP E 126 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE E 149 " --> pdb=" O CYS E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'F' and resid 5 through 20 Processing helix chain 'F' and resid 36 through 41 removed outlier: 4.001A pdb=" N VAL F 40 " --> pdb=" O PRO F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 97 removed outlier: 3.801A pdb=" N ARG F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 166 removed outlier: 3.737A pdb=" N VAL F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 49 Processing helix chain 'G' and resid 50 through 60 Processing helix chain 'G' and resid 68 through 85 removed outlier: 3.555A pdb=" N LYS G 72 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 99 through 115 removed outlier: 3.950A pdb=" N GLU G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 136 Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.870A pdb=" N ILE G 141 " --> pdb=" O GLY G 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 61 removed outlier: 4.219A pdb=" N SER H 60 " --> pdb=" O ASP H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.515A pdb=" N LEU H 65 " --> pdb=" O ARG H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 78 through 92 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.747A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 172 through 175 removed outlier: 3.919A pdb=" N ILE H 175 " --> pdb=" O PRO H 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 172 through 175' Processing helix chain 'H' and resid 181 through 197 Processing helix chain 'H' and resid 202 through 216 Processing helix chain 'H' and resid 222 through 232 Processing helix chain 'H' and resid 252 through 257 removed outlier: 3.683A pdb=" N CYS H 257 " --> pdb=" O GLU H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 263 removed outlier: 4.272A pdb=" N PHE H 262 " --> pdb=" O PRO H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 267 Processing helix chain 'H' and resid 273 through 285 removed outlier: 3.542A pdb=" N CYS H 285 " --> pdb=" O SER H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 296 removed outlier: 4.130A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 321 Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 337 through 349 Processing helix chain 'H' and resid 350 through 355 removed outlier: 3.855A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 368 through 373 removed outlier: 3.797A pdb=" N ARG H 372 " --> pdb=" O SER H 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 61 Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU I 65 " --> pdb=" O ARG I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.747A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 146 Processing helix chain 'I' and resid 172 through 175 removed outlier: 3.919A pdb=" N ILE I 175 " --> pdb=" O PRO I 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 172 through 175' Processing helix chain 'I' and resid 181 through 197 Processing helix chain 'I' and resid 202 through 216 Processing helix chain 'I' and resid 222 through 232 Processing helix chain 'I' and resid 252 through 257 removed outlier: 3.683A pdb=" N CYS I 257 " --> pdb=" O GLU I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 263 removed outlier: 4.271A pdb=" N PHE I 262 " --> pdb=" O PRO I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 267 Processing helix chain 'I' and resid 273 through 285 removed outlier: 3.543A pdb=" N CYS I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 296 removed outlier: 4.130A pdb=" N LYS I 291 " --> pdb=" O ILE I 287 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP I 292 " --> pdb=" O ASP I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 321 Processing helix chain 'I' and resid 334 through 336 No H-bonds generated for 'chain 'I' and resid 334 through 336' Processing helix chain 'I' and resid 337 through 349 Processing helix chain 'I' and resid 350 through 355 removed outlier: 3.855A pdb=" N GLN I 354 " --> pdb=" O THR I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 366 Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.798A pdb=" N ARG I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'J' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU J 65 " --> pdb=" O ARG J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 62 through 65' Processing helix chain 'J' and resid 78 through 92 Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.747A pdb=" N ARG J 116 " --> pdb=" O PRO J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 146 Processing helix chain 'J' and resid 172 through 175 removed outlier: 3.920A pdb=" N ILE J 175 " --> pdb=" O PRO J 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 172 through 175' Processing helix chain 'J' and resid 181 through 197 Processing helix chain 'J' and resid 202 through 216 Processing helix chain 'J' and resid 222 through 232 Processing helix chain 'J' and resid 252 through 257 removed outlier: 3.683A pdb=" N CYS J 257 " --> pdb=" O GLU J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 263 removed outlier: 4.272A pdb=" N PHE J 262 " --> pdb=" O PRO J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 267 Processing helix chain 'J' and resid 273 through 285 removed outlier: 3.542A pdb=" N CYS J 285 " --> pdb=" O SER J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 296 removed outlier: 4.130A pdb=" N LYS J 291 " --> pdb=" O ILE J 287 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP J 292 " --> pdb=" O ASP J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 321 Processing helix chain 'J' and resid 334 through 336 No H-bonds generated for 'chain 'J' and resid 334 through 336' Processing helix chain 'J' and resid 337 through 349 Processing helix chain 'J' and resid 350 through 355 removed outlier: 3.855A pdb=" N GLN J 354 " --> pdb=" O THR J 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 366 Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.797A pdb=" N ARG J 372 " --> pdb=" O SER J 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 61 Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU K 65 " --> pdb=" O ARG K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 78 through 92 Processing helix chain 'K' and resid 112 through 126 removed outlier: 3.747A pdb=" N ARG K 116 " --> pdb=" O PRO K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 146 Processing helix chain 'K' and resid 172 through 175 removed outlier: 3.919A pdb=" N ILE K 175 " --> pdb=" O PRO K 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 172 through 175' Processing helix chain 'K' and resid 181 through 197 Processing helix chain 'K' and resid 202 through 216 Processing helix chain 'K' and resid 222 through 232 Processing helix chain 'K' and resid 252 through 257 removed outlier: 3.684A pdb=" N CYS K 257 " --> pdb=" O GLU K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 263 removed outlier: 4.272A pdb=" N PHE K 262 " --> pdb=" O PRO K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 267 Processing helix chain 'K' and resid 273 through 285 removed outlier: 3.543A pdb=" N CYS K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 296 removed outlier: 4.130A pdb=" N LYS K 291 " --> pdb=" O ILE K 287 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP K 292 " --> pdb=" O ASP K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 334 through 336 No H-bonds generated for 'chain 'K' and resid 334 through 336' Processing helix chain 'K' and resid 337 through 349 Processing helix chain 'K' and resid 350 through 355 removed outlier: 3.856A pdb=" N GLN K 354 " --> pdb=" O THR K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 366 Processing helix chain 'K' and resid 368 through 373 removed outlier: 3.797A pdb=" N ARG K 372 " --> pdb=" O SER K 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 61 Processing helix chain 'L' and resid 62 through 65 removed outlier: 3.515A pdb=" N LEU L 65 " --> pdb=" O ARG L 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 62 through 65' Processing helix chain 'L' and resid 78 through 92 Processing helix chain 'L' and resid 112 through 126 removed outlier: 3.746A pdb=" N ARG L 116 " --> pdb=" O PRO L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 146 Processing helix chain 'L' and resid 172 through 175 removed outlier: 3.919A pdb=" N ILE L 175 " --> pdb=" O PRO L 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 172 through 175' Processing helix chain 'L' and resid 181 through 197 Processing helix chain 'L' and resid 202 through 216 Processing helix chain 'L' and resid 222 through 232 Processing helix chain 'L' and resid 252 through 257 removed outlier: 3.683A pdb=" N CYS L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 263 removed outlier: 4.272A pdb=" N PHE L 262 " --> pdb=" O PRO L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 267 Processing helix chain 'L' and resid 273 through 285 removed outlier: 3.543A pdb=" N CYS L 285 " --> pdb=" O SER L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 296 removed outlier: 4.130A pdb=" N LYS L 291 " --> pdb=" O ILE L 287 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP L 292 " --> pdb=" O ASP L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 321 Processing helix chain 'L' and resid 334 through 336 No H-bonds generated for 'chain 'L' and resid 334 through 336' Processing helix chain 'L' and resid 337 through 349 Processing helix chain 'L' and resid 350 through 355 removed outlier: 3.855A pdb=" N GLN L 354 " --> pdb=" O THR L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 366 Processing helix chain 'L' and resid 368 through 373 removed outlier: 3.797A pdb=" N ARG L 372 " --> pdb=" O SER L 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 61 Processing helix chain 'M' and resid 62 through 65 removed outlier: 3.515A pdb=" N LEU M 65 " --> pdb=" O ARG M 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 62 through 65' Processing helix chain 'M' and resid 78 through 92 Processing helix chain 'M' and resid 112 through 126 removed outlier: 3.747A pdb=" N ARG M 116 " --> pdb=" O PRO M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 146 Processing helix chain 'M' and resid 172 through 175 removed outlier: 3.919A pdb=" N ILE M 175 " --> pdb=" O PRO M 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 172 through 175' Processing helix chain 'M' and resid 181 through 197 Processing helix chain 'M' and resid 202 through 216 Processing helix chain 'M' and resid 222 through 232 Processing helix chain 'M' and resid 252 through 257 removed outlier: 3.683A pdb=" N CYS M 257 " --> pdb=" O GLU M 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 263 removed outlier: 4.271A pdb=" N PHE M 262 " --> pdb=" O PRO M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 267 Processing helix chain 'M' and resid 273 through 285 removed outlier: 3.543A pdb=" N CYS M 285 " --> pdb=" O SER M 281 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 296 removed outlier: 4.131A pdb=" N LYS M 291 " --> pdb=" O ILE M 287 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP M 292 " --> pdb=" O ASP M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 321 Processing helix chain 'M' and resid 334 through 336 No H-bonds generated for 'chain 'M' and resid 334 through 336' Processing helix chain 'M' and resid 337 through 349 Processing helix chain 'M' and resid 350 through 355 removed outlier: 3.855A pdb=" N GLN M 354 " --> pdb=" O THR M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 366 Processing helix chain 'M' and resid 368 through 373 removed outlier: 3.797A pdb=" N ARG M 372 " --> pdb=" O SER M 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 61 Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.515A pdb=" N LEU N 65 " --> pdb=" O ARG N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 78 through 92 Processing helix chain 'N' and resid 112 through 126 removed outlier: 3.747A pdb=" N ARG N 116 " --> pdb=" O PRO N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 146 Processing helix chain 'N' and resid 172 through 175 removed outlier: 3.919A pdb=" N ILE N 175 " --> pdb=" O PRO N 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 172 through 175' Processing helix chain 'N' and resid 181 through 197 Processing helix chain 'N' and resid 202 through 216 Processing helix chain 'N' and resid 222 through 232 Processing helix chain 'N' and resid 252 through 257 removed outlier: 3.683A pdb=" N CYS N 257 " --> pdb=" O GLU N 253 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 263 removed outlier: 4.272A pdb=" N PHE N 262 " --> pdb=" O PRO N 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 264 through 267 Processing helix chain 'N' and resid 273 through 285 removed outlier: 3.542A pdb=" N CYS N 285 " --> pdb=" O SER N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 296 removed outlier: 4.130A pdb=" N LYS N 291 " --> pdb=" O ILE N 287 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP N 292 " --> pdb=" O ASP N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 321 Processing helix chain 'N' and resid 334 through 336 No H-bonds generated for 'chain 'N' and resid 334 through 336' Processing helix chain 'N' and resid 337 through 349 Processing helix chain 'N' and resid 350 through 355 removed outlier: 3.856A pdb=" N GLN N 354 " --> pdb=" O THR N 351 " (cutoff:3.500A) Processing helix chain 'N' and resid 359 through 366 Processing helix chain 'N' and resid 368 through 373 removed outlier: 3.798A pdb=" N ARG N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 61 Processing helix chain 'O' and resid 78 through 92 Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.746A pdb=" N ARG O 116 " --> pdb=" O PRO O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 146 Processing helix chain 'O' and resid 172 through 175 removed outlier: 3.919A pdb=" N ILE O 175 " --> pdb=" O PRO O 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 172 through 175' Processing helix chain 'O' and resid 181 through 197 Processing helix chain 'O' and resid 202 through 216 Processing helix chain 'O' and resid 222 through 232 Processing helix chain 'O' and resid 252 through 257 removed outlier: 3.683A pdb=" N CYS O 257 " --> pdb=" O GLU O 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 258 through 263 removed outlier: 4.272A pdb=" N PHE O 262 " --> pdb=" O PRO O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 264 through 267 Processing helix chain 'O' and resid 273 through 285 removed outlier: 3.542A pdb=" N CYS O 285 " --> pdb=" O SER O 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 296 removed outlier: 4.130A pdb=" N LYS O 291 " --> pdb=" O ILE O 287 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP O 292 " --> pdb=" O ASP O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 321 Processing helix chain 'O' and resid 334 through 336 No H-bonds generated for 'chain 'O' and resid 334 through 336' Processing helix chain 'O' and resid 337 through 349 Processing helix chain 'O' and resid 350 through 355 removed outlier: 3.856A pdb=" N GLN O 354 " --> pdb=" O THR O 351 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 366 Processing helix chain 'O' and resid 368 through 373 removed outlier: 3.797A pdb=" N ARG O 372 " --> pdb=" O SER O 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 61 Processing helix chain 'P' and resid 62 through 65 removed outlier: 3.515A pdb=" N LEU P 65 " --> pdb=" O ARG P 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 62 through 65' Processing helix chain 'P' and resid 78 through 92 Processing helix chain 'P' and resid 112 through 126 removed outlier: 3.747A pdb=" N ARG P 116 " --> pdb=" O PRO P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 146 Processing helix chain 'P' and resid 172 through 175 removed outlier: 3.919A pdb=" N ILE P 175 " --> pdb=" O PRO P 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 172 through 175' Processing helix chain 'P' and resid 181 through 197 Processing helix chain 'P' and resid 202 through 216 Processing helix chain 'P' and resid 222 through 232 Processing helix chain 'P' and resid 252 through 257 removed outlier: 3.684A pdb=" N CYS P 257 " --> pdb=" O GLU P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 258 through 263 removed outlier: 4.271A pdb=" N PHE P 262 " --> pdb=" O PRO P 258 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 267 Processing helix chain 'P' and resid 273 through 285 removed outlier: 3.543A pdb=" N CYS P 285 " --> pdb=" O SER P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 286 through 296 removed outlier: 4.129A pdb=" N LYS P 291 " --> pdb=" O ILE P 287 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP P 292 " --> pdb=" O ASP P 288 " (cutoff:3.500A) Processing helix chain 'P' and resid 308 through 321 Processing helix chain 'P' and resid 334 through 336 No H-bonds generated for 'chain 'P' and resid 334 through 336' Processing helix chain 'P' and resid 337 through 349 Processing helix chain 'P' and resid 350 through 355 removed outlier: 3.856A pdb=" N GLN P 354 " --> pdb=" O THR P 351 " (cutoff:3.500A) Processing helix chain 'P' and resid 359 through 365 removed outlier: 3.775A pdb=" N ALA P 365 " --> pdb=" O GLU P 361 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 61 Processing helix chain 'Q' and resid 62 through 65 removed outlier: 3.515A pdb=" N LEU Q 65 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 62 through 65' Processing helix chain 'Q' and resid 78 through 92 Processing helix chain 'Q' and resid 112 through 126 removed outlier: 3.747A pdb=" N ARG Q 116 " --> pdb=" O PRO Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 146 Processing helix chain 'Q' and resid 172 through 175 removed outlier: 3.919A pdb=" N ILE Q 175 " --> pdb=" O PRO Q 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 172 through 175' Processing helix chain 'Q' and resid 181 through 197 Processing helix chain 'Q' and resid 202 through 216 Processing helix chain 'Q' and resid 222 through 232 Processing helix chain 'Q' and resid 252 through 257 removed outlier: 3.683A pdb=" N CYS Q 257 " --> pdb=" O GLU Q 253 " (cutoff:3.500A) Processing helix chain 'Q' and resid 258 through 263 removed outlier: 4.272A pdb=" N PHE Q 262 " --> pdb=" O PRO Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 267 Processing helix chain 'Q' and resid 273 through 285 removed outlier: 3.543A pdb=" N CYS Q 285 " --> pdb=" O SER Q 281 " (cutoff:3.500A) Processing helix chain 'Q' and resid 286 through 296 removed outlier: 4.129A pdb=" N LYS Q 291 " --> pdb=" O ILE Q 287 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP Q 292 " --> pdb=" O ASP Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 308 through 321 Processing helix chain 'Q' and resid 334 through 336 No H-bonds generated for 'chain 'Q' and resid 334 through 336' Processing helix chain 'Q' and resid 337 through 349 Processing helix chain 'Q' and resid 350 through 355 removed outlier: 3.855A pdb=" N GLN Q 354 " --> pdb=" O THR Q 351 " (cutoff:3.500A) Processing helix chain 'Q' and resid 359 through 366 Processing helix chain 'Q' and resid 368 through 373 removed outlier: 3.797A pdb=" N ARG Q 372 " --> pdb=" O SER Q 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 61 Processing helix chain 'R' and resid 62 through 65 removed outlier: 3.515A pdb=" N LEU R 65 " --> pdb=" O ARG R 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 62 through 65' Processing helix chain 'R' and resid 78 through 92 Processing helix chain 'R' and resid 112 through 126 removed outlier: 3.747A pdb=" N ARG R 116 " --> pdb=" O PRO R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 146 Processing helix chain 'R' and resid 172 through 175 removed outlier: 3.919A pdb=" N ILE R 175 " --> pdb=" O PRO R 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 172 through 175' Processing helix chain 'R' and resid 181 through 197 Processing helix chain 'R' and resid 202 through 216 Processing helix chain 'R' and resid 222 through 232 Processing helix chain 'R' and resid 252 through 257 removed outlier: 3.683A pdb=" N CYS R 257 " --> pdb=" O GLU R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 263 removed outlier: 4.272A pdb=" N PHE R 262 " --> pdb=" O PRO R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 267 Processing helix chain 'R' and resid 273 through 285 removed outlier: 3.543A pdb=" N CYS R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 296 removed outlier: 4.129A pdb=" N LYS R 291 " --> pdb=" O ILE R 287 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP R 292 " --> pdb=" O ASP R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 321 Processing helix chain 'R' and resid 334 through 336 No H-bonds generated for 'chain 'R' and resid 334 through 336' Processing helix chain 'R' and resid 337 through 349 Processing helix chain 'R' and resid 350 through 355 removed outlier: 3.856A pdb=" N GLN R 354 " --> pdb=" O THR R 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 366 Processing helix chain 'R' and resid 368 through 373 removed outlier: 3.797A pdb=" N ARG R 372 " --> pdb=" O SER R 368 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 61 Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU S 65 " --> pdb=" O ARG S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 78 through 92 Processing helix chain 'S' and resid 112 through 126 removed outlier: 3.747A pdb=" N ARG S 116 " --> pdb=" O PRO S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 146 Processing helix chain 'S' and resid 172 through 175 removed outlier: 3.919A pdb=" N ILE S 175 " --> pdb=" O PRO S 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 172 through 175' Processing helix chain 'S' and resid 181 through 197 Processing helix chain 'S' and resid 202 through 216 Processing helix chain 'S' and resid 222 through 232 Processing helix chain 'S' and resid 252 through 257 removed outlier: 3.683A pdb=" N CYS S 257 " --> pdb=" O GLU S 253 " (cutoff:3.500A) Processing helix chain 'S' and resid 258 through 263 removed outlier: 4.272A pdb=" N PHE S 262 " --> pdb=" O PRO S 258 " (cutoff:3.500A) Processing helix chain 'S' and resid 264 through 267 Processing helix chain 'S' and resid 273 through 285 removed outlier: 3.542A pdb=" N CYS S 285 " --> pdb=" O SER S 281 " (cutoff:3.500A) Processing helix chain 'S' and resid 286 through 296 removed outlier: 4.130A pdb=" N LYS S 291 " --> pdb=" O ILE S 287 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP S 292 " --> pdb=" O ASP S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 308 through 321 Processing helix chain 'S' and resid 334 through 336 No H-bonds generated for 'chain 'S' and resid 334 through 336' Processing helix chain 'S' and resid 337 through 349 Processing helix chain 'S' and resid 350 through 355 removed outlier: 3.855A pdb=" N GLN S 354 " --> pdb=" O THR S 351 " (cutoff:3.500A) Processing helix chain 'S' and resid 359 through 366 Processing helix chain 'S' and resid 368 through 373 removed outlier: 3.797A pdb=" N ARG S 372 " --> pdb=" O SER S 368 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 61 Processing helix chain 'T' and resid 62 through 65 removed outlier: 3.515A pdb=" N LEU T 65 " --> pdb=" O ARG T 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 62 through 65' Processing helix chain 'T' and resid 78 through 92 Processing helix chain 'T' and resid 112 through 126 removed outlier: 3.747A pdb=" N ARG T 116 " --> pdb=" O PRO T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 137 through 146 Processing helix chain 'T' and resid 172 through 175 removed outlier: 3.919A pdb=" N ILE T 175 " --> pdb=" O PRO T 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 172 through 175' Processing helix chain 'T' and resid 181 through 197 Processing helix chain 'T' and resid 202 through 216 Processing helix chain 'T' and resid 222 through 232 Processing helix chain 'T' and resid 252 through 257 removed outlier: 3.683A pdb=" N CYS T 257 " --> pdb=" O GLU T 253 " (cutoff:3.500A) Processing helix chain 'T' and resid 258 through 263 removed outlier: 4.271A pdb=" N PHE T 262 " --> pdb=" O PRO T 258 " (cutoff:3.500A) Processing helix chain 'T' and resid 264 through 267 Processing helix chain 'T' and resid 273 through 285 removed outlier: 3.543A pdb=" N CYS T 285 " --> pdb=" O SER T 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 286 through 296 removed outlier: 4.129A pdb=" N LYS T 291 " --> pdb=" O ILE T 287 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP T 292 " --> pdb=" O ASP T 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 308 through 321 Processing helix chain 'T' and resid 334 through 336 No H-bonds generated for 'chain 'T' and resid 334 through 336' Processing helix chain 'T' and resid 337 through 349 Processing helix chain 'T' and resid 350 through 355 removed outlier: 3.855A pdb=" N GLN T 354 " --> pdb=" O THR T 351 " (cutoff:3.500A) Processing helix chain 'T' and resid 359 through 366 Processing helix chain 'T' and resid 368 through 373 removed outlier: 3.798A pdb=" N ARG T 372 " --> pdb=" O SER T 368 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 61 Processing helix chain 'U' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU U 65 " --> pdb=" O ARG U 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 62 through 65' Processing helix chain 'U' and resid 78 through 92 Processing helix chain 'U' and resid 112 through 126 removed outlier: 3.746A pdb=" N ARG U 116 " --> pdb=" O PRO U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 137 through 146 Processing helix chain 'U' and resid 172 through 175 removed outlier: 3.919A pdb=" N ILE U 175 " --> pdb=" O PRO U 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 172 through 175' Processing helix chain 'U' and resid 181 through 197 Processing helix chain 'U' and resid 202 through 216 Processing helix chain 'U' and resid 222 through 232 Processing helix chain 'U' and resid 252 through 257 removed outlier: 3.684A pdb=" N CYS U 257 " --> pdb=" O GLU U 253 " (cutoff:3.500A) Processing helix chain 'U' and resid 258 through 263 removed outlier: 4.272A pdb=" N PHE U 262 " --> pdb=" O PRO U 258 " (cutoff:3.500A) Processing helix chain 'U' and resid 264 through 267 Processing helix chain 'U' and resid 273 through 285 removed outlier: 3.542A pdb=" N CYS U 285 " --> pdb=" O SER U 281 " (cutoff:3.500A) Processing helix chain 'U' and resid 286 through 296 removed outlier: 4.130A pdb=" N LYS U 291 " --> pdb=" O ILE U 287 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP U 292 " --> pdb=" O ASP U 288 " (cutoff:3.500A) Processing helix chain 'U' and resid 308 through 321 Processing helix chain 'U' and resid 334 through 336 No H-bonds generated for 'chain 'U' and resid 334 through 336' Processing helix chain 'U' and resid 337 through 349 Processing helix chain 'U' and resid 350 through 355 removed outlier: 3.856A pdb=" N GLN U 354 " --> pdb=" O THR U 351 " (cutoff:3.500A) Processing helix chain 'U' and resid 359 through 366 Processing helix chain 'U' and resid 368 through 373 removed outlier: 3.798A pdb=" N ARG U 372 " --> pdb=" O SER U 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.540A pdb=" N ASP A 11 " --> pdb=" O LYS A 18 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 20 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR A 113 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 110 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 142 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 185 removed outlier: 3.700A pdb=" N THR A 175 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 193 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 177 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS A 191 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 185 removed outlier: 7.425A pdb=" N THR A 166 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE A 319 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 254 through 256 removed outlier: 3.639A pdb=" N LYS A 254 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 33 removed outlier: 3.720A pdb=" N HIS B 30 " --> pdb=" O CYS B 20 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS B 20 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 19 " --> pdb=" O ASP B 12 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 57 removed outlier: 4.215A pdb=" N MET B 56 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY B 37 " --> pdb=" O MET B 56 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B 38 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 57 removed outlier: 4.215A pdb=" N MET B 56 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY B 37 " --> pdb=" O MET B 56 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 41 " --> pdb=" O TYR E 58 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 74 through 75 removed outlier: 4.166A pdb=" N GLU B 75 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 78 " --> pdb=" O GLU B 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 135 through 136 removed outlier: 3.774A pdb=" N VAL B 136 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 155 through 156 removed outlier: 6.461A pdb=" N VAL B 155 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 301 " --> pdb=" O GLU B 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.579A pdb=" N TYR B 170 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.839A pdb=" N SER C 355 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR C 347 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 14 through 16 removed outlier: 7.322A pdb=" N VAL C 32 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLU C 47 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE C 34 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 55 through 60 removed outlier: 3.729A pdb=" N ASP C 59 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 68 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR C 85 " --> pdb=" O LYS C 82 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 55 through 60 removed outlier: 3.729A pdb=" N ASP C 59 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 68 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA C 76 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 99 through 103 removed outlier: 4.063A pdb=" N CYS C 101 " --> pdb=" O GLY C 114 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR C 124 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL C 133 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 145 through 150 removed outlier: 3.639A pdb=" N SER C 147 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 157 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG C 167 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE C 168 " --> pdb=" O MET C 195 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET C 195 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 208 through 209 Processing sheet with id=AC1, first strand: chain 'C' and resid 257 through 260 Processing sheet with id=AC2, first strand: chain 'D' and resid 32 through 37 removed outlier: 3.992A pdb=" N VAL D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS D 44 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET D 56 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 55 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER D 94 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 85 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 142 through 143 removed outlier: 3.517A pdb=" N ALA D 142 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR D 153 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS D 157 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG D 160 " --> pdb=" O LYS D 157 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY D 221 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR D 224 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 199 " --> pdb=" O THR D 224 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AC5, first strand: chain 'F' and resid 51 through 52 removed outlier: 3.642A pdb=" N VAL F 72 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.522A pdb=" N PHE H 31 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR H 106 " --> pdb=" O CYS H 10 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN H 12 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR H 133 " --> pdb=" O THR H 103 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AC8, first strand: chain 'H' and resid 176 through 178 removed outlier: 3.509A pdb=" N MET H 176 " --> pdb=" O ASN H 162 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER H 300 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU H 153 " --> pdb=" O SER H 300 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 165 through 166 Processing sheet with id=AD1, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AD2, first strand: chain 'I' and resid 29 through 32 removed outlier: 3.522A pdb=" N PHE I 31 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR I 106 " --> pdb=" O CYS I 10 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN I 12 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR I 133 " --> pdb=" O THR I 103 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 35 through 36 Processing sheet with id=AD4, first strand: chain 'I' and resid 71 through 72 Processing sheet with id=AD5, first strand: chain 'I' and resid 176 through 178 removed outlier: 3.510A pdb=" N MET I 176 " --> pdb=" O ASN I 162 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE I 151 " --> pdb=" O VAL I 298 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER I 300 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU I 153 " --> pdb=" O SER I 300 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 165 through 166 Processing sheet with id=AD7, first strand: chain 'I' and resid 238 through 241 Processing sheet with id=AD8, first strand: chain 'J' and resid 29 through 32 removed outlier: 3.522A pdb=" N PHE J 31 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR J 106 " --> pdb=" O CYS J 10 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN J 12 " --> pdb=" O THR J 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR J 133 " --> pdb=" O THR J 103 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 35 through 36 Processing sheet with id=AE1, first strand: chain 'J' and resid 71 through 72 Processing sheet with id=AE2, first strand: chain 'J' and resid 176 through 178 removed outlier: 3.510A pdb=" N MET J 176 " --> pdb=" O ASN J 162 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE J 151 " --> pdb=" O VAL J 298 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER J 300 " --> pdb=" O ILE J 151 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU J 153 " --> pdb=" O SER J 300 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 165 through 166 Processing sheet with id=AE4, first strand: chain 'J' and resid 238 through 241 Processing sheet with id=AE5, first strand: chain 'K' and resid 29 through 32 removed outlier: 3.522A pdb=" N PHE K 31 " --> pdb=" O VAL K 17 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR K 106 " --> pdb=" O CYS K 10 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN K 12 " --> pdb=" O THR K 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR K 133 " --> pdb=" O THR K 103 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 35 through 36 Processing sheet with id=AE7, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AE8, first strand: chain 'K' and resid 176 through 178 removed outlier: 3.509A pdb=" N MET K 176 " --> pdb=" O ASN K 162 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE K 151 " --> pdb=" O VAL K 298 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER K 300 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU K 153 " --> pdb=" O SER K 300 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 165 through 166 Processing sheet with id=AF1, first strand: chain 'K' and resid 238 through 241 Processing sheet with id=AF2, first strand: chain 'L' and resid 29 through 32 removed outlier: 3.522A pdb=" N PHE L 31 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR L 106 " --> pdb=" O CYS L 10 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN L 12 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR L 133 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 35 through 36 Processing sheet with id=AF4, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AF5, first strand: chain 'L' and resid 176 through 178 removed outlier: 3.511A pdb=" N MET L 176 " --> pdb=" O ASN L 162 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE L 151 " --> pdb=" O VAL L 298 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER L 300 " --> pdb=" O ILE L 151 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU L 153 " --> pdb=" O SER L 300 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 165 through 166 Processing sheet with id=AF7, first strand: chain 'L' and resid 238 through 241 Processing sheet with id=AF8, first strand: chain 'M' and resid 29 through 31 removed outlier: 3.598A pdb=" N PHE M 31 " --> pdb=" O VAL M 17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR M 106 " --> pdb=" O CYS M 10 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR M 133 " --> pdb=" O THR M 103 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AG1, first strand: chain 'M' and resid 71 through 72 Processing sheet with id=AG2, first strand: chain 'M' and resid 176 through 178 removed outlier: 3.510A pdb=" N MET M 176 " --> pdb=" O ASN M 162 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE M 151 " --> pdb=" O VAL M 298 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER M 300 " --> pdb=" O ILE M 151 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU M 153 " --> pdb=" O SER M 300 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 165 through 166 Processing sheet with id=AG4, first strand: chain 'M' and resid 238 through 241 Processing sheet with id=AG5, first strand: chain 'N' and resid 29 through 32 removed outlier: 3.523A pdb=" N PHE N 31 " --> pdb=" O VAL N 17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR N 106 " --> pdb=" O CYS N 10 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN N 12 " --> pdb=" O THR N 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR N 133 " --> pdb=" O THR N 103 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 35 through 36 Processing sheet with id=AG7, first strand: chain 'N' and resid 71 through 72 Processing sheet with id=AG8, first strand: chain 'N' and resid 176 through 178 removed outlier: 3.509A pdb=" N MET N 176 " --> pdb=" O ASN N 162 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE N 151 " --> pdb=" O VAL N 298 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER N 300 " --> pdb=" O ILE N 151 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU N 153 " --> pdb=" O SER N 300 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 165 through 166 Processing sheet with id=AH1, first strand: chain 'N' and resid 238 through 241 Processing sheet with id=AH2, first strand: chain 'O' and resid 29 through 32 removed outlier: 3.522A pdb=" N PHE O 31 " --> pdb=" O VAL O 17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR O 106 " --> pdb=" O CYS O 10 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN O 12 " --> pdb=" O THR O 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR O 133 " --> pdb=" O THR O 103 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 53 through 54 removed outlier: 3.614A pdb=" N VAL O 35 " --> pdb=" O LYS O 68 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG O 37 " --> pdb=" O THR O 66 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR O 66 " --> pdb=" O ARG O 37 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 71 through 72 Processing sheet with id=AH5, first strand: chain 'O' and resid 176 through 178 removed outlier: 3.509A pdb=" N MET O 176 " --> pdb=" O ASN O 162 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE O 151 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER O 300 " --> pdb=" O ILE O 151 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU O 153 " --> pdb=" O SER O 300 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 165 through 166 Processing sheet with id=AH7, first strand: chain 'O' and resid 238 through 241 Processing sheet with id=AH8, first strand: chain 'P' and resid 29 through 32 removed outlier: 3.523A pdb=" N PHE P 31 " --> pdb=" O VAL P 17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR P 106 " --> pdb=" O CYS P 10 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN P 12 " --> pdb=" O THR P 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR P 133 " --> pdb=" O THR P 103 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'P' and resid 35 through 36 Processing sheet with id=AI1, first strand: chain 'P' and resid 71 through 72 Processing sheet with id=AI2, first strand: chain 'P' and resid 176 through 178 removed outlier: 3.509A pdb=" N MET P 176 " --> pdb=" O ASN P 162 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE P 151 " --> pdb=" O VAL P 298 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER P 300 " --> pdb=" O ILE P 151 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU P 153 " --> pdb=" O SER P 300 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'P' and resid 165 through 166 Processing sheet with id=AI4, first strand: chain 'P' and resid 238 through 241 Processing sheet with id=AI5, first strand: chain 'Q' and resid 29 through 32 removed outlier: 3.547A pdb=" N PHE Q 31 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR Q 106 " --> pdb=" O CYS Q 10 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR Q 133 " --> pdb=" O THR Q 103 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Q' and resid 35 through 36 Processing sheet with id=AI7, first strand: chain 'Q' and resid 71 through 72 Processing sheet with id=AI8, first strand: chain 'Q' and resid 176 through 178 removed outlier: 3.510A pdb=" N MET Q 176 " --> pdb=" O ASN Q 162 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE Q 151 " --> pdb=" O VAL Q 298 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER Q 300 " --> pdb=" O ILE Q 151 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU Q 153 " --> pdb=" O SER Q 300 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Q' and resid 165 through 166 Processing sheet with id=AJ1, first strand: chain 'Q' and resid 238 through 241 Processing sheet with id=AJ2, first strand: chain 'R' and resid 29 through 32 removed outlier: 3.522A pdb=" N PHE R 31 " --> pdb=" O VAL R 17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR R 106 " --> pdb=" O CYS R 10 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN R 12 " --> pdb=" O THR R 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR R 133 " --> pdb=" O THR R 103 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'R' and resid 35 through 36 Processing sheet with id=AJ4, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AJ5, first strand: chain 'R' and resid 176 through 178 removed outlier: 3.510A pdb=" N MET R 176 " --> pdb=" O ASN R 162 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE R 151 " --> pdb=" O VAL R 298 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER R 300 " --> pdb=" O ILE R 151 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU R 153 " --> pdb=" O SER R 300 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'R' and resid 165 through 166 Processing sheet with id=AJ7, first strand: chain 'R' and resid 238 through 241 Processing sheet with id=AJ8, first strand: chain 'S' and resid 29 through 32 removed outlier: 3.523A pdb=" N PHE S 31 " --> pdb=" O VAL S 17 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR S 106 " --> pdb=" O CYS S 10 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN S 12 " --> pdb=" O THR S 106 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR S 133 " --> pdb=" O THR S 103 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'S' and resid 35 through 36 Processing sheet with id=AK1, first strand: chain 'S' and resid 71 through 72 Processing sheet with id=AK2, first strand: chain 'S' and resid 176 through 178 removed outlier: 3.509A pdb=" N MET S 176 " --> pdb=" O ASN S 162 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE S 151 " --> pdb=" O VAL S 298 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER S 300 " --> pdb=" O ILE S 151 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU S 153 " --> pdb=" O SER S 300 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'S' and resid 165 through 166 Processing sheet with id=AK4, first strand: chain 'S' and resid 238 through 241 Processing sheet with id=AK5, first strand: chain 'T' and resid 29 through 32 removed outlier: 3.522A pdb=" N PHE T 31 " --> pdb=" O VAL T 17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR T 106 " --> pdb=" O CYS T 10 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN T 12 " --> pdb=" O THR T 106 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR T 133 " --> pdb=" O THR T 103 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'T' and resid 35 through 36 Processing sheet with id=AK7, first strand: chain 'T' and resid 71 through 72 Processing sheet with id=AK8, first strand: chain 'T' and resid 176 through 178 removed outlier: 3.509A pdb=" N MET T 176 " --> pdb=" O ASN T 162 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE T 151 " --> pdb=" O VAL T 298 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER T 300 " --> pdb=" O ILE T 151 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU T 153 " --> pdb=" O SER T 300 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'T' and resid 165 through 166 Processing sheet with id=AL1, first strand: chain 'T' and resid 238 through 241 Processing sheet with id=AL2, first strand: chain 'U' and resid 29 through 32 removed outlier: 3.523A pdb=" N PHE U 31 " --> pdb=" O VAL U 17 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR U 106 " --> pdb=" O CYS U 10 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN U 12 " --> pdb=" O THR U 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR U 133 " --> pdb=" O THR U 103 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'U' and resid 35 through 36 Processing sheet with id=AL4, first strand: chain 'U' and resid 71 through 72 Processing sheet with id=AL5, first strand: chain 'U' and resid 176 through 178 removed outlier: 3.510A pdb=" N MET U 176 " --> pdb=" O ASN U 162 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE U 151 " --> pdb=" O VAL U 298 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER U 300 " --> pdb=" O ILE U 151 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU U 153 " --> pdb=" O SER U 300 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'U' and resid 165 through 166 Processing sheet with id=AL7, first strand: chain 'U' and resid 238 through 241 2427 hydrogen bonds defined for protein. 6681 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: 24.75 Time building geometry restraints manager: 15.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8869 1.31 - 1.44: 12947 1.44 - 1.58: 29267 1.58 - 1.71: 98 1.71 - 1.84: 435 Bond restraints: 51616 Sorted by residual: bond pdb=" CA LYS P 359 " pdb=" C LYS P 359 " ideal model delta sigma weight residual 1.522 1.416 0.107 1.39e-02 5.18e+03 5.87e+01 bond pdb=" C5 ADP O 501 " pdb=" C6 ADP O 501 " ideal model delta sigma weight residual 1.490 1.350 0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" O2A ADP T 501 " pdb=" PA ADP T 501 " ideal model delta sigma weight residual 1.510 1.649 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C5 ADP S 501 " pdb=" C6 ADP S 501 " ideal model delta sigma weight residual 1.490 1.351 0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C5 ADP M 501 " pdb=" C6 ADP M 501 " ideal model delta sigma weight residual 1.490 1.351 0.139 2.00e-02 2.50e+03 4.81e+01 ... (remaining 51611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 69078 2.76 - 5.53: 943 5.53 - 8.29: 195 8.29 - 11.05: 152 11.05 - 13.81: 33 Bond angle restraints: 70401 Sorted by residual: angle pdb=" N SER Q 14 " pdb=" CA SER Q 14 " pdb=" C SER Q 14 " ideal model delta sigma weight residual 113.15 99.54 13.61 1.19e+00 7.06e-01 1.31e+02 angle pdb=" N LEU B 193 " pdb=" CA LEU B 193 " pdb=" C LEU B 193 " ideal model delta sigma weight residual 111.28 98.90 12.38 1.09e+00 8.42e-01 1.29e+02 angle pdb=" N SER P 368 " pdb=" CA SER P 368 " pdb=" C SER P 368 " ideal model delta sigma weight residual 113.02 101.26 11.76 1.20e+00 6.94e-01 9.61e+01 angle pdb=" N ILE O 64 " pdb=" CA ILE O 64 " pdb=" C ILE O 64 " ideal model delta sigma weight residual 113.47 123.30 -9.83 1.01e+00 9.80e-01 9.46e+01 angle pdb=" N VAL H 43 " pdb=" CA VAL H 43 " pdb=" C VAL H 43 " ideal model delta sigma weight residual 110.62 120.35 -9.73 1.02e+00 9.61e-01 9.11e+01 ... (remaining 70396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.46: 30279 34.46 - 68.91: 495 68.91 - 103.37: 38 103.37 - 137.83: 21 137.83 - 172.28: 7 Dihedral angle restraints: 30840 sinusoidal: 10023 harmonic: 20817 Sorted by residual: dihedral pdb=" O2A ADP H 401 " pdb=" O3A ADP H 401 " pdb=" PA ADP H 401 " pdb=" PB ADP H 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.28 -172.28 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP T 501 " pdb=" O5' ADP T 501 " pdb=" PA ADP T 501 " pdb=" O2A ADP T 501 " ideal model delta sinusoidal sigma weight residual -60.00 89.54 -149.54 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1B ADP A 502 " pdb=" O3A ADP A 502 " pdb=" PB ADP A 502 " pdb=" PA ADP A 502 " ideal model delta sinusoidal sigma weight residual 300.00 152.75 147.24 1 2.00e+01 2.50e-03 4.42e+01 ... (remaining 30837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 7482 0.092 - 0.183: 649 0.183 - 0.275: 35 0.275 - 0.366: 6 0.366 - 0.458: 5 Chirality restraints: 8177 Sorted by residual: chirality pdb=" CA MET O 44 " pdb=" N MET O 44 " pdb=" C MET O 44 " pdb=" CB MET O 44 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.24e+00 chirality pdb=" CA TYR O 53 " pdb=" N TYR O 53 " pdb=" C TYR O 53 " pdb=" CB TYR O 53 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CA MET H 47 " pdb=" N MET H 47 " pdb=" C MET H 47 " pdb=" CB MET H 47 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 8174 not shown) Planarity restraints: 9240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU I 361 " 0.017 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" CD GLU I 361 " -0.061 2.00e-02 2.50e+03 pdb=" OE1 GLU I 361 " 0.022 2.00e-02 2.50e+03 pdb=" OE2 GLU I 361 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR P 358 " 0.015 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C THR P 358 " -0.057 2.00e-02 2.50e+03 pdb=" O THR P 358 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS P 359 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR P 362 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C TYR P 362 " 0.050 2.00e-02 2.50e+03 pdb=" O TYR P 362 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP P 363 " -0.017 2.00e-02 2.50e+03 ... (remaining 9237 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 220 2.38 - 3.01: 31046 3.01 - 3.64: 74390 3.64 - 4.27: 101575 4.27 - 4.90: 172407 Nonbonded interactions: 379638 Sorted by model distance: nonbonded pdb=" CD1 TRP k 1 " pdb=" SG CYS k 5 " model vdw 1.752 3.620 nonbonded pdb=" CD1 TRP l 1 " pdb=" SG CYS l 5 " model vdw 1.752 3.620 nonbonded pdb=" CD1 TRP c 1 " pdb=" SG CYS c 5 " model vdw 1.752 3.620 nonbonded pdb=" CD1 TRP n 1 " pdb=" SG CYS n 5 " model vdw 1.752 3.620 nonbonded pdb=" CD1 TRP h 1 " pdb=" SG CYS h 5 " model vdw 1.752 3.620 ... (remaining 379633 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 'H' and ((resid 5 through 12 and (name N or name CA or name C or name O o \ r name CB )) or resid 13 or (resid 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 or (resid 16 through 19 and (name N or name CA or nam \ e C or name O or name CB )) or resid 20 or (resid 21 through 22 and (name N or n \ ame CA or name C or name O or name CB )) or resid 23 or (resid 24 through 35 and \ (name N or name CA or name C or name O or name CB )) or resid 36 or (resid 37 t \ hrough 41 and (name N or name CA or name C or name O or name CB )) or resid 42 o \ r (resid 43 through 45 and (name N or name CA or name C or name O or name CB )) \ or resid 46 or (resid 47 and (name N or name CA or name C or name O or name CB ) \ ) or resid 48 or (resid 49 through 54 and (name N or name CA or name C or name O \ or name CB )) or resid 55 or (resid 56 through 62 and (name N or name CA or nam \ e C or name O or name CB )) or resid 63 or (resid 64 through 73 and (name N or n \ ame CA or name C or name O or name CB )) or resid 74 or (resid 75 through 145 an \ d (name N or name CA or name C or name O or name CB )) or resid 146 or (resid 14 \ 7 through 149 and (name N or name CA or name C or name O or name CB )) or resid \ 150 or (resid 151 through 155 and (name N or name CA or name C or name O or name \ CB )) or resid 156 or (resid 157 and (name N or name CA or name C or name O or \ name CB )) or resid 158 or (resid 159 through 167 and (name N or name CA or name \ C or name O or name CB )) or resid 168 or (resid 169 through 181 and (name N or \ name CA or name C or name O or name CB )) or resid 182 or (resid 183 through 19 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 197 or (resi \ d 198 through 244 and (name N or name CA or name C or name O or name CB )) or re \ sid 245 or (resid 246 through 250 and (name N or name CA or name C or name O or \ name CB )) or resid 251 or (resid 252 through 267 and (name N or name CA or name \ C or name O or name CB )) or resid 268 or (resid 269 through 272 and (name N or \ name CA or name C or name O or name CB )) or resid 273 or (resid 274 through 30 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 301 through \ 302 or (resid 303 through 307 and (name N or name CA or name C or name O or name \ CB )) or resid 308 or (resid 309 through 341 and (name N or name CA or name C o \ r name O or name CB )) or resid 342 through 343 or (resid 344 through 365 and (n \ ame N or name CA or name C or name O or name CB )) or resid 366 or (resid 367 th \ rough 374 and (name N or name CA or name C or name O or name CB )) or (resid 375 \ and (name N or name CA or name C or name O or name CB or name OXT)))) selection = (chain 'I' and ((resid 5 through 12 and (name N or name CA or name C or name O o \ r name CB )) or resid 13 or (resid 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 or (resid 16 through 19 and (name N or name CA or nam \ e C or name O or name CB )) or resid 20 or (resid 21 through 22 and (name N or n \ ame CA or name C or name O or name CB )) or resid 23 or (resid 24 through 35 and \ (name N or name CA or name C or name O or name CB )) or resid 36 or (resid 37 t \ hrough 41 and (name N or name CA or name C or name O or name CB )) or resid 42 o \ r (resid 43 through 45 and (name N or name CA or name C or name O or name CB )) \ or resid 46 or (resid 47 and (name N or name CA or name C or name O or name CB ) \ ) or resid 48 or (resid 49 through 54 and (name N or name CA or name C or name O \ or name CB )) or resid 55 or (resid 56 through 62 and (name N or name CA or nam \ e C or name O or name CB )) or resid 63 or (resid 64 through 73 and (name N or n \ ame CA or name C or name O or name CB )) or resid 74 or (resid 75 through 145 an \ d (name N or name CA or name C or name O or name CB )) or resid 146 or (resid 14 \ 7 through 149 and (name N or name CA or name C or name O or name CB )) or resid \ 150 or (resid 151 through 155 and (name N or name CA or name C or name O or name \ CB )) or resid 156 or (resid 157 and (name N or name CA or name C or name O or \ name CB )) or resid 158 or (resid 159 through 167 and (name N or name CA or name \ C or name O or name CB )) or resid 168 or (resid 169 through 181 and (name N or \ name CA or name C or name O or name CB )) or resid 182 or (resid 183 through 19 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 197 or (resi \ d 198 through 244 and (name N or name CA or name C or name O or name CB )) or re \ sid 245 or (resid 246 through 250 and (name N or name CA or name C or name O or \ name CB )) or resid 251 or (resid 252 through 267 and (name N or name CA or name \ C or name O or name CB )) or resid 268 or (resid 269 through 272 and (name N or \ name CA or name C or name O or name CB )) or resid 273 or (resid 274 through 30 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 301 through \ 302 or (resid 303 through 307 and (name N or name CA or name C or name O or name \ CB )) or resid 308 or (resid 309 through 341 and (name N or name CA or name C o \ r name O or name CB )) or resid 342 through 343 or (resid 344 through 365 and (n \ ame N or name CA or name C or name O or name CB )) or resid 366 or (resid 367 th \ rough 374 and (name N or name CA or name C or name O or name CB )) or (resid 375 \ and (name N or name CA or name C or name O or name CB or name OXT)))) selection = (chain 'J' and resid 5 through 375) selection = (chain 'K' and resid 5 through 375) selection = (chain 'L' and resid 5 through 375) selection = (chain 'M' and ((resid 5 through 181 and (name N or name CA or name C or name O \ or name CB )) or resid 182 through 375)) selection = (chain 'N' and ((resid 5 through 12 and (name N or name CA or name C or name O o \ r name CB )) or resid 13 or (resid 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 or (resid 16 through 19 and (name N or name CA or nam \ e C or name O or name CB )) or resid 20 or (resid 21 through 22 and (name N or n \ ame CA or name C or name O or name CB )) or resid 23 or (resid 24 through 35 and \ (name N or name CA or name C or name O or name CB )) or resid 36 or (resid 37 t \ hrough 41 and (name N or name CA or name C or name O or name CB )) or resid 42 o \ r (resid 43 through 45 and (name N or name CA or name C or name O or name CB )) \ or resid 46 or (resid 47 and (name N or name CA or name C or name O or name CB ) \ ) or resid 48 or (resid 49 through 54 and (name N or name CA or name C or name O \ or name CB )) or resid 55 or (resid 56 through 62 and (name N or name CA or nam \ e C or name O or name CB )) or resid 63 or (resid 64 through 73 and (name N or n \ ame CA or name C or name O or name CB )) or resid 74 or (resid 75 through 145 an \ d (name N or name CA or name C or name O or name CB )) or resid 146 or (resid 14 \ 7 through 149 and (name N or name CA or name C or name O or name CB )) or resid \ 150 or (resid 151 through 155 and (name N or name CA or name C or name O or name \ CB )) or resid 156 or (resid 157 and (name N or name CA or name C or name O or \ name CB )) or resid 158 or (resid 159 through 167 and (name N or name CA or name \ C or name O or name CB )) or resid 168 or (resid 169 through 181 and (name N or \ name CA or name C or name O or name CB )) or resid 182 or (resid 183 through 19 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 197 or (resi \ d 198 through 244 and (name N or name CA or name C or name O or name CB )) or re \ sid 245 or (resid 246 through 250 and (name N or name CA or name C or name O or \ name CB )) or resid 251 or (resid 252 through 267 and (name N or name CA or name \ C or name O or name CB )) or resid 268 or (resid 269 through 272 and (name N or \ name CA or name C or name O or name CB )) or resid 273 or (resid 274 through 30 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 301 through \ 302 or (resid 303 through 307 and (name N or name CA or name C or name O or name \ CB )) or resid 308 or (resid 309 through 341 and (name N or name CA or name C o \ r name O or name CB )) or resid 342 through 343 or (resid 344 through 365 and (n \ ame N or name CA or name C or name O or name CB )) or resid 366 or (resid 367 th \ rough 374 and (name N or name CA or name C or name O or name CB )) or (resid 375 \ and (name N or name CA or name C or name O or name CB or name OXT)))) selection = (chain 'O' and ((resid 5 through 12 and (name N or name CA or name C or name O o \ r name CB )) or resid 13 or (resid 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 or (resid 16 through 19 and (name N or name CA or nam \ e C or name O or name CB )) or resid 20 or (resid 21 through 22 and (name N or n \ ame CA or name C or name O or name CB )) or resid 23 or (resid 24 through 35 and \ (name N or name CA or name C or name O or name CB )) or resid 36 or (resid 37 t \ hrough 41 and (name N or name CA or name C or name O or name CB )) or resid 42 o \ r (resid 43 through 45 and (name N or name CA or name C or name O or name CB )) \ or resid 46 or (resid 47 and (name N or name CA or name C or name O or name CB ) \ ) or resid 48 or (resid 49 through 54 and (name N or name CA or name C or name O \ or name CB )) or resid 55 or (resid 56 through 62 and (name N or name CA or nam \ e C or name O or name CB )) or resid 63 or (resid 64 through 73 and (name N or n \ ame CA or name C or name O or name CB )) or resid 74 or (resid 75 through 145 an \ d (name N or name CA or name C or name O or name CB )) or resid 146 or (resid 14 \ 7 through 149 and (name N or name CA or name C or name O or name CB )) or resid \ 150 or (resid 151 through 155 and (name N or name CA or name C or name O or name \ CB )) or resid 156 or (resid 157 and (name N or name CA or name C or name O or \ name CB )) or resid 158 or (resid 159 through 167 and (name N or name CA or name \ C or name O or name CB )) or resid 168 or (resid 169 through 181 and (name N or \ name CA or name C or name O or name CB )) or resid 182 or (resid 183 through 19 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 197 or (resi \ d 198 through 244 and (name N or name CA or name C or name O or name CB )) or re \ sid 245 or (resid 246 through 250 and (name N or name CA or name C or name O or \ name CB )) or resid 251 or (resid 252 through 267 and (name N or name CA or name \ C or name O or name CB )) or resid 268 or (resid 269 through 272 and (name N or \ name CA or name C or name O or name CB )) or resid 273 or (resid 274 through 30 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 301 through \ 302 or (resid 303 through 307 and (name N or name CA or name C or name O or name \ CB )) or resid 308 or (resid 309 through 341 and (name N or name CA or name C o \ r name O or name CB )) or resid 342 through 343 or (resid 344 through 365 and (n \ ame N or name CA or name C or name O or name CB )) or resid 366 or (resid 367 th \ rough 374 and (name N or name CA or name C or name O or name CB )) or (resid 375 \ and (name N or name CA or name C or name O or name CB or name OXT)))) selection = (chain 'P' and ((resid 5 through 12 and (name N or name CA or name C or name O o \ r name CB )) or resid 13 or (resid 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 or (resid 16 through 19 and (name N or name CA or nam \ e C or name O or name CB )) or resid 20 or (resid 21 through 22 and (name N or n \ ame CA or name C or name O or name CB )) or resid 23 or (resid 24 through 35 and \ (name N or name CA or name C or name O or name CB )) or resid 36 or (resid 37 t \ hrough 41 and (name N or name CA or name C or name O or name CB )) or resid 42 o \ r (resid 43 through 45 and (name N or name CA or name C or name O or name CB )) \ or resid 46 or (resid 47 and (name N or name CA or name C or name O or name CB ) \ ) or resid 48 or (resid 49 through 54 and (name N or name CA or name C or name O \ or name CB )) or resid 55 or (resid 56 through 62 and (name N or name CA or nam \ e C or name O or name CB )) or resid 63 or (resid 64 through 73 and (name N or n \ ame CA or name C or name O or name CB )) or resid 74 or (resid 75 through 145 an \ d (name N or name CA or name C or name O or name CB )) or resid 146 or (resid 14 \ 7 through 149 and (name N or name CA or name C or name O or name CB )) or resid \ 150 or (resid 151 through 155 and (name N or name CA or name C or name O or name \ CB )) or resid 156 or (resid 157 and (name N or name CA or name C or name O or \ name CB )) or resid 158 or (resid 159 through 167 and (name N or name CA or name \ C or name O or name CB )) or resid 168 or (resid 169 through 181 and (name N or \ name CA or name C or name O or name CB )) or resid 182 or (resid 183 through 19 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 197 or (resi \ d 198 through 244 and (name N or name CA or name C or name O or name CB )) or re \ sid 245 or (resid 246 through 250 and (name N or name CA or name C or name O or \ name CB )) or resid 251 or (resid 252 through 267 and (name N or name CA or name \ C or name O or name CB )) or resid 268 or (resid 269 through 272 and (name N or \ name CA or name C or name O or name CB )) or resid 273 or (resid 274 through 30 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 301 through \ 302 or (resid 303 through 307 and (name N or name CA or name C or name O or name \ CB )) or resid 308 or (resid 309 through 341 and (name N or name CA or name C o \ r name O or name CB )) or resid 342 through 343 or (resid 344 through 365 and (n \ ame N or name CA or name C or name O or name CB )) or resid 366 or (resid 367 th \ rough 374 and (name N or name CA or name C or name O or name CB )) or (resid 375 \ and (name N or name CA or name C or name O or name CB or name OXT)))) selection = (chain 'Q' and ((resid 5 through 12 and (name N or name CA or name C or name O o \ r name CB )) or resid 13 or (resid 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 or (resid 16 through 19 and (name N or name CA or nam \ e C or name O or name CB )) or resid 20 or (resid 21 through 22 and (name N or n \ ame CA or name C or name O or name CB )) or resid 23 or (resid 24 through 35 and \ (name N or name CA or name C or name O or name CB )) or resid 36 or (resid 37 t \ hrough 41 and (name N or name CA or name C or name O or name CB )) or resid 42 o \ r (resid 43 through 45 and (name N or name CA or name C or name O or name CB )) \ or resid 46 or (resid 47 and (name N or name CA or name C or name O or name CB ) \ ) or resid 48 or (resid 49 through 54 and (name N or name CA or name C or name O \ or name CB )) or resid 55 or (resid 56 through 62 and (name N or name CA or nam \ e C or name O or name CB )) or resid 63 or (resid 64 through 73 and (name N or n \ ame CA or name C or name O or name CB )) or resid 74 or (resid 75 through 145 an \ d (name N or name CA or name C or name O or name CB )) or resid 146 or (resid 14 \ 7 through 149 and (name N or name CA or name C or name O or name CB )) or resid \ 150 or (resid 151 through 155 and (name N or name CA or name C or name O or name \ CB )) or resid 156 or (resid 157 and (name N or name CA or name C or name O or \ name CB )) or resid 158 or (resid 159 through 167 and (name N or name CA or name \ C or name O or name CB )) or resid 168 or (resid 169 through 181 and (name N or \ name CA or name C or name O or name CB )) or resid 182 or (resid 183 through 19 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 197 or (resi \ d 198 through 244 and (name N or name CA or name C or name O or name CB )) or re \ sid 245 or (resid 246 through 250 and (name N or name CA or name C or name O or \ name CB )) or resid 251 or (resid 252 through 267 and (name N or name CA or name \ C or name O or name CB )) or resid 268 or (resid 269 through 272 and (name N or \ name CA or name C or name O or name CB )) or resid 273 or (resid 274 through 30 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 301 through \ 302 or (resid 303 through 307 and (name N or name CA or name C or name O or name \ CB )) or resid 308 or (resid 309 through 341 and (name N or name CA or name C o \ r name O or name CB )) or resid 342 through 343 or (resid 344 through 365 and (n \ ame N or name CA or name C or name O or name CB )) or resid 366 or (resid 367 th \ rough 374 and (name N or name CA or name C or name O or name CB )) or (resid 375 \ and (name N or name CA or name C or name O or name CB or name OXT)))) selection = (chain 'R' and ((resid 5 through 12 and (name N or name CA or name C or name O o \ r name CB )) or resid 13 or (resid 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 or (resid 16 through 19 and (name N or name CA or nam \ e C or name O or name CB )) or resid 20 or (resid 21 through 22 and (name N or n \ ame CA or name C or name O or name CB )) or resid 23 or (resid 24 through 35 and \ (name N or name CA or name C or name O or name CB )) or resid 36 or (resid 37 t \ hrough 41 and (name N or name CA or name C or name O or name CB )) or resid 42 o \ r (resid 43 through 45 and (name N or name CA or name C or name O or name CB )) \ or resid 46 or (resid 47 and (name N or name CA or name C or name O or name CB ) \ ) or resid 48 or (resid 49 through 54 and (name N or name CA or name C or name O \ or name CB )) or resid 55 or (resid 56 through 62 and (name N or name CA or nam \ e C or name O or name CB )) or resid 63 or (resid 64 through 73 and (name N or n \ ame CA or name C or name O or name CB )) or resid 74 or (resid 75 through 145 an \ d (name N or name CA or name C or name O or name CB )) or resid 146 or (resid 14 \ 7 through 149 and (name N or name CA or name C or name O or name CB )) or resid \ 150 or (resid 151 through 155 and (name N or name CA or name C or name O or name \ CB )) or resid 156 or (resid 157 and (name N or name CA or name C or name O or \ name CB )) or resid 158 or (resid 159 through 167 and (name N or name CA or name \ C or name O or name CB )) or resid 168 or (resid 169 through 181 and (name N or \ name CA or name C or name O or name CB )) or resid 182 or (resid 183 through 19 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 197 or (resi \ d 198 through 244 and (name N or name CA or name C or name O or name CB )) or re \ sid 245 or (resid 246 through 250 and (name N or name CA or name C or name O or \ name CB )) or resid 251 or (resid 252 through 267 and (name N or name CA or name \ C or name O or name CB )) or resid 268 or (resid 269 through 272 and (name N or \ name CA or name C or name O or name CB )) or resid 273 or (resid 274 through 30 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 301 through \ 302 or (resid 303 through 307 and (name N or name CA or name C or name O or name \ CB )) or resid 308 or (resid 309 through 341 and (name N or name CA or name C o \ r name O or name CB )) or resid 342 through 343 or (resid 344 through 365 and (n \ ame N or name CA or name C or name O or name CB )) or resid 366 or (resid 367 th \ rough 374 and (name N or name CA or name C or name O or name CB )) or (resid 375 \ and (name N or name CA or name C or name O or name CB or name OXT)))) selection = (chain 'S' and ((resid 5 through 12 and (name N or name CA or name C or name O o \ r name CB )) or resid 13 or (resid 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 or (resid 16 through 19 and (name N or name CA or nam \ e C or name O or name CB )) or resid 20 or (resid 21 through 22 and (name N or n \ ame CA or name C or name O or name CB )) or resid 23 or (resid 24 through 35 and \ (name N or name CA or name C or name O or name CB )) or resid 36 or (resid 37 t \ hrough 41 and (name N or name CA or name C or name O or name CB )) or resid 42 o \ r (resid 43 through 45 and (name N or name CA or name C or name O or name CB )) \ or resid 46 or (resid 47 and (name N or name CA or name C or name O or name CB ) \ ) or resid 48 or (resid 49 through 54 and (name N or name CA or name C or name O \ or name CB )) or resid 55 or (resid 56 through 62 and (name N or name CA or nam \ e C or name O or name CB )) or resid 63 or (resid 64 through 73 and (name N or n \ ame CA or name C or name O or name CB )) or resid 74 or (resid 75 through 145 an \ d (name N or name CA or name C or name O or name CB )) or resid 146 or (resid 14 \ 7 through 149 and (name N or name CA or name C or name O or name CB )) or resid \ 150 or (resid 151 through 155 and (name N or name CA or name C or name O or name \ CB )) or resid 156 or (resid 157 and (name N or name CA or name C or name O or \ name CB )) or resid 158 or (resid 159 through 167 and (name N or name CA or name \ C or name O or name CB )) or resid 168 or (resid 169 through 181 and (name N or \ name CA or name C or name O or name CB )) or resid 182 or (resid 183 through 19 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 197 or (resi \ d 198 through 244 and (name N or name CA or name C or name O or name CB )) or re \ sid 245 or (resid 246 through 250 and (name N or name CA or name C or name O or \ name CB )) or resid 251 or (resid 252 through 267 and (name N or name CA or name \ C or name O or name CB )) or resid 268 or (resid 269 through 272 and (name N or \ name CA or name C or name O or name CB )) or resid 273 or (resid 274 through 30 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 301 through \ 302 or (resid 303 through 307 and (name N or name CA or name C or name O or name \ CB )) or resid 308 or (resid 309 through 341 and (name N or name CA or name C o \ r name O or name CB )) or resid 342 through 343 or (resid 344 through 365 and (n \ ame N or name CA or name C or name O or name CB )) or resid 366 or (resid 367 th \ rough 374 and (name N or name CA or name C or name O or name CB )) or (resid 375 \ and (name N or name CA or name C or name O or name CB or name OXT)))) selection = (chain 'T' and resid 5 through 375) selection = (chain 'U' and resid 5 through 375) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 2.530 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: 0.100 Extract box with map and model: 2.030 Check model and map are aligned: 0.390 Set scattering table: 0.450 Process input model: 119.760 Find NCS groups from input model: 4.870 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 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 : 0.009 0.140 51616 Z= 0.663 Angle : 0.891 13.813 70401 Z= 0.448 Chirality : 0.048 0.458 8177 Planarity : 0.003 0.059 9210 Dihedral : 14.374 172.282 17340 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.45 % Allowed : 0.26 % Favored : 99.28 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.11), residues: 7041 helix: 2.02 (0.10), residues: 2693 sheet: 0.95 (0.18), residues: 975 loop : -0.28 (0.11), residues: 3373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP b 1 HIS 0.009 0.001 HIS H 40 PHE 0.015 0.001 PHE H 375 TYR 0.036 0.001 TYR O 53 ARG 0.006 0.000 ARG O 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14082 Ramachandran restraints generated. 7041 Oldfield, 0 Emsley, 7041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14082 Ramachandran restraints generated. 7041 Oldfield, 0 Emsley, 7041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1292 residues out of total 6097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 1273 time to evaluate : 4.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8093 (p0) cc_final: 0.7573 (p0) REVERT: A 110 PHE cc_start: 0.5950 (m-10) cc_final: 0.5261 (m-10) REVERT: A 114 GLU cc_start: 0.7572 (pm20) cc_final: 0.7305 (pm20) REVERT: A 135 ASN cc_start: 0.7791 (m110) cc_final: 0.7516 (m-40) REVERT: A 233 TYR cc_start: 0.5336 (p90) cc_final: 0.4184 (p90) REVERT: A 244 LYS cc_start: 0.7105 (ttmm) cc_final: 0.6877 (ttmm) REVERT: A 292 PHE cc_start: 0.6974 (t80) cc_final: 0.6749 (t80) REVERT: A 326 THR cc_start: 0.7691 (p) cc_final: 0.7369 (p) REVERT: A 354 SER cc_start: 0.7832 (m) cc_final: 0.7611 (m) REVERT: B 66 SER cc_start: 0.8235 (p) cc_final: 0.7742 (p) REVERT: B 86 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7874 (ttpp) REVERT: B 106 LYS cc_start: 0.8085 (mmtm) cc_final: 0.7744 (mmtp) REVERT: B 145 THR cc_start: 0.6584 (p) cc_final: 0.6345 (p) REVERT: B 146 LEU cc_start: 0.7244 (mp) cc_final: 0.6696 (mp) REVERT: B 158 ASP cc_start: 0.7238 (t0) cc_final: 0.7020 (t0) REVERT: B 226 ASN cc_start: 0.8088 (t0) cc_final: 0.7722 (t0) REVERT: B 263 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6106 (mm-30) REVERT: B 280 GLU cc_start: 0.5372 (tm-30) cc_final: 0.5073 (tm-30) REVERT: B 296 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7267 (tp30) REVERT: C 42 TRP cc_start: 0.8032 (m100) cc_final: 0.7122 (m100) REVERT: C 95 ILE cc_start: 0.8143 (mm) cc_final: 0.7781 (mm) REVERT: C 104 TRP cc_start: 0.7202 (m100) cc_final: 0.6790 (m100) REVERT: C 148 LEU cc_start: 0.8147 (mp) cc_final: 0.7911 (mp) REVERT: C 191 PHE cc_start: 0.7739 (t80) cc_final: 0.7460 (t80) REVERT: C 300 GLU cc_start: 0.5445 (tm-30) cc_final: 0.5206 (tm-30) REVERT: C 301 ARG cc_start: 0.7754 (ttm-80) cc_final: 0.7460 (ttm-80) REVERT: C 358 ASP cc_start: 0.7739 (m-30) cc_final: 0.7483 (m-30) REVERT: D 37 ASP cc_start: 0.5871 (m-30) cc_final: 0.5599 (m-30) REVERT: D 61 LEU cc_start: 0.6226 (mt) cc_final: 0.5997 (mt) REVERT: D 92 ASN cc_start: 0.6157 (m110) cc_final: 0.5750 (m-40) REVERT: D 156 SER cc_start: 0.7862 (t) cc_final: 0.7368 (t) REVERT: D 231 HIS cc_start: 0.6553 (p90) cc_final: 0.6281 (p90) REVERT: D 247 PHE cc_start: 0.6626 (t80) cc_final: 0.6357 (t80) REVERT: D 259 LYS cc_start: 0.8809 (ttmm) cc_final: 0.8599 (ttmm) REVERT: E 14 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7930 (mmmt) REVERT: E 60 ILE cc_start: 0.7546 (pt) cc_final: 0.7160 (pt) REVERT: E 95 MET cc_start: 0.7570 (mtm) cc_final: 0.7329 (mtm) REVERT: E 155 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8603 (mmtm) REVERT: F 64 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7621 (mm-30) REVERT: F 91 MET cc_start: 0.7400 (mmt) cc_final: 0.6923 (mmm) REVERT: F 95 MET cc_start: 0.5282 (mmp) cc_final: 0.4782 (mmp) REVERT: F 99 GLU cc_start: 0.7217 (pm20) cc_final: 0.6908 (pm20) REVERT: F 163 GLU cc_start: 0.6733 (tm-30) cc_final: 0.6457 (tm-30) REVERT: H 18 LYS cc_start: 0.7909 (mppt) cc_final: 0.7327 (mmmm) REVERT: H 82 MET cc_start: 0.7754 (tpt) cc_final: 0.7481 (tpt) REVERT: H 276 GLU cc_start: 0.7012 (tp30) cc_final: 0.6573 (tp30) REVERT: I 72 GLU cc_start: 0.6658 (tt0) cc_final: 0.6385 (pt0) REVERT: I 105 LEU cc_start: 0.6752 (tt) cc_final: 0.6503 (tp) REVERT: I 107 GLU cc_start: 0.6289 (pm20) cc_final: 0.5757 (pm20) REVERT: I 214 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7299 (tt0) REVERT: I 215 LYS cc_start: 0.8313 (mtmt) cc_final: 0.8109 (ttmm) REVERT: I 238 LYS cc_start: 0.6657 (mttp) cc_final: 0.6401 (mtmm) REVERT: I 283 MET cc_start: 0.6211 (ptp) cc_final: 0.5949 (ptp) REVERT: I 363 ASP cc_start: 0.7316 (m-30) cc_final: 0.7092 (m-30) REVERT: N 119 MET cc_start: 0.6624 (ttm) cc_final: 0.6212 (ttp) REVERT: N 154 ASP cc_start: 0.7269 (t0) cc_final: 0.6624 (t0) REVERT: N 176 MET cc_start: 0.6768 (mtp) cc_final: 0.6407 (mtt) REVERT: N 185 LEU cc_start: 0.6103 (mm) cc_final: 0.5573 (tp) REVERT: N 191 LYS cc_start: 0.7597 (tptt) cc_final: 0.7180 (tppt) REVERT: N 244 ASP cc_start: 0.7295 (p0) cc_final: 0.7089 (p0) REVERT: N 288 ASP cc_start: 0.6495 (t0) cc_final: 0.6290 (t0) REVERT: O 18 LYS cc_start: 0.7760 (mttp) cc_final: 0.7495 (mttp) REVERT: O 62 ARG cc_start: 0.7601 (ptt-90) cc_final: 0.7124 (ptt-90) REVERT: O 195 GLU cc_start: 0.7391 (pt0) cc_final: 0.7162 (pt0) REVERT: O 227 MET cc_start: 0.7646 (mmm) cc_final: 0.7304 (mmm) REVERT: O 255 PHE cc_start: 0.7607 (p90) cc_final: 0.7395 (p90) REVERT: O 328 LYS cc_start: 0.7257 (tptt) cc_final: 0.7053 (tptt) REVERT: P 52 SER cc_start: 0.7403 (m) cc_final: 0.7103 (t) REVERT: P 91 TYR cc_start: 0.7701 (m-80) cc_final: 0.7066 (m-80) REVERT: P 111 ASN cc_start: 0.7285 (m-40) cc_final: 0.6864 (m-40) REVERT: P 123 MET cc_start: 0.6990 (mmm) cc_final: 0.6641 (mmm) REVERT: P 153 LEU cc_start: 0.7600 (mp) cc_final: 0.7354 (mp) REVERT: P 214 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6812 (mt-10) REVERT: P 215 LYS cc_start: 0.7348 (mtmm) cc_final: 0.7063 (mtmm) REVERT: P 226 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6828 (mm-30) REVERT: P 335 ARG cc_start: 0.8114 (ptt-90) cc_final: 0.7883 (ptp-170) REVERT: Q 12 ASN cc_start: 0.8163 (m-40) cc_final: 0.7906 (m-40) REVERT: Q 69 TYR cc_start: 0.7828 (m-80) cc_final: 0.7587 (m-80) REVERT: Q 136 ILE cc_start: 0.6813 (mm) cc_final: 0.6518 (mm) REVERT: Q 161 HIS cc_start: 0.5511 (p90) cc_final: 0.5210 (p90) REVERT: Q 171 LEU cc_start: 0.7883 (mm) cc_final: 0.7662 (mp) REVERT: Q 208 ILE cc_start: 0.7871 (mm) cc_final: 0.7650 (mt) REVERT: Q 210 ARG cc_start: 0.7320 (ttm-80) cc_final: 0.6986 (ttm-80) REVERT: Q 255 PHE cc_start: 0.6402 (p90) cc_final: 0.6084 (p90) REVERT: Q 300 SER cc_start: 0.7850 (m) cc_final: 0.7521 (p) REVERT: Q 325 MET cc_start: 0.7214 (pmm) cc_final: 0.5912 (ptp) REVERT: R 176 MET cc_start: 0.7409 (mtt) cc_final: 0.7135 (mtp) REVERT: R 248 ILE cc_start: 0.8627 (mm) cc_final: 0.8137 (tt) REVERT: R 259 GLU cc_start: 0.6280 (tm-30) cc_final: 0.6019 (tm-30) REVERT: R 313 MET cc_start: 0.5103 (tpt) cc_final: 0.4798 (tpt) REVERT: R 346 LEU cc_start: 0.7834 (tt) cc_final: 0.7615 (tt) REVERT: R 359 LYS cc_start: 0.7466 (tttp) cc_final: 0.7177 (tttp) REVERT: R 364 GLU cc_start: 0.8189 (pp20) cc_final: 0.7957 (pp20) REVERT: S 66 THR cc_start: 0.7308 (m) cc_final: 0.7046 (p) REVERT: S 120 THR cc_start: 0.7548 (m) cc_final: 0.7063 (t) REVERT: S 176 MET cc_start: 0.6338 (mmm) cc_final: 0.5898 (mmm) REVERT: S 334 GLU cc_start: 0.6048 (pm20) cc_final: 0.5729 (pm20) REVERT: e 5 CYS cc_start: 0.4439 (OUTLIER) cc_final: 0.4198 (t) REVERT: n 5 CYS cc_start: 0.1995 (OUTLIER) cc_final: 0.1775 (p) outliers start: 19 outliers final: 13 residues processed: 1291 average time/residue: 0.5692 time to fit residues: 1211.3822 Evaluate side-chains 1162 residues out of total 6097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 1147 time to evaluate : 4.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 24 PHE Chi-restraints excluded: chain a residue 5 CYS Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain c residue 5 CYS Chi-restraints excluded: chain d residue 5 CYS Chi-restraints excluded: chain e residue 5 CYS Chi-restraints excluded: chain f residue 5 CYS Chi-restraints excluded: chain g residue 5 CYS Chi-restraints excluded: chain h residue 5 CYS Chi-restraints excluded: chain i residue 5 CYS Chi-restraints excluded: chain j residue 5 CYS Chi-restraints excluded: chain l residue 5 CYS Chi-restraints excluded: chain m residue 5 CYS Chi-restraints excluded: chain n residue 5 CYS Chi-restraints excluded: chain o residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 597 optimal weight: 0.7980 chunk 535 optimal weight: 0.9980 chunk 297 optimal weight: 30.0000 chunk 183 optimal weight: 1.9990 chunk 361 optimal weight: 50.0000 chunk 286 optimal weight: 9.9990 chunk 554 optimal weight: 0.0970 chunk 214 optimal weight: 1.9990 chunk 336 optimal weight: 40.0000 chunk 412 optimal weight: 0.8980 chunk 642 optimal weight: 0.4980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 269 HIS B 323 GLN C 65 ASN D 252 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 360 GLN ** O 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 87 HIS O 121 GLN P 121 GLN P 296 ASN Q 173 HIS R 173 HIS S 246 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 51616 Z= 0.210 Angle : 0.667 11.141 70401 Z= 0.330 Chirality : 0.047 0.211 8177 Planarity : 0.004 0.051 9210 Dihedral : 9.774 175.260 8023 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.96 % Allowed : 11.54 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.00 (0.10), residues: 7041 helix: 1.71 (0.10), residues: 2644 sheet: 0.83 (0.17), residues: 1083 loop : -0.20 (0.11), residues: 3314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP n 1 HIS 0.014 0.002 HIS P 275 PHE 0.024 0.002 PHE P 255 TYR 0.024 0.001 TYR B 192 ARG 0.025 0.001 ARG N 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14082 Ramachandran restraints generated. 7041 Oldfield, 0 Emsley, 7041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14082 Ramachandran restraints generated. 7041 Oldfield, 0 Emsley, 7041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 6097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 1206 time to evaluate : 4.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6202 (mp10) REVERT: A 89 MET cc_start: 0.7906 (tpp) cc_final: 0.7667 (tpp) REVERT: A 99 LYS cc_start: 0.7453 (mtpp) cc_final: 0.6877 (mtmm) REVERT: A 114 GLU cc_start: 0.7480 (pm20) cc_final: 0.7254 (pm20) REVERT: A 135 ASN cc_start: 0.7877 (m110) cc_final: 0.7523 (m-40) REVERT: A 280 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7155 (mm-30) REVERT: A 305 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7392 (mm-40) REVERT: A 402 GLU cc_start: 0.7308 (pm20) cc_final: 0.7095 (pm20) REVERT: B 74 MET cc_start: 0.6179 (mmp) cc_final: 0.5884 (mmp) REVERT: B 86 LYS cc_start: 0.8284 (ttpp) cc_final: 0.7928 (ttpp) REVERT: B 146 LEU cc_start: 0.7472 (mp) cc_final: 0.7177 (mp) REVERT: B 158 ASP cc_start: 0.7155 (t0) cc_final: 0.6937 (t0) REVERT: B 226 ASN cc_start: 0.8152 (t0) cc_final: 0.7850 (t0) REVERT: B 257 GLU cc_start: 0.7412 (mp0) cc_final: 0.7174 (mp0) REVERT: B 263 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6308 (tp30) REVERT: C 42 TRP cc_start: 0.7963 (m100) cc_final: 0.6972 (m100) REVERT: C 56 THR cc_start: 0.8021 (p) cc_final: 0.7730 (m) REVERT: C 94 ARG cc_start: 0.7072 (mtt180) cc_final: 0.6776 (mtt180) REVERT: C 95 ILE cc_start: 0.7996 (mm) cc_final: 0.7753 (mm) REVERT: C 104 TRP cc_start: 0.7433 (m100) cc_final: 0.6654 (m100) REVERT: C 108 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6585 (mm-30) REVERT: C 148 LEU cc_start: 0.8116 (mp) cc_final: 0.7871 (mt) REVERT: C 300 GLU cc_start: 0.5503 (tm-30) cc_final: 0.5154 (tm-30) REVERT: C 358 ASP cc_start: 0.7840 (m-30) cc_final: 0.7638 (m-30) REVERT: D 184 GLU cc_start: 0.6955 (mp0) cc_final: 0.6644 (mp0) REVERT: D 247 PHE cc_start: 0.6582 (t80) cc_final: 0.6232 (t80) REVERT: D 261 TYR cc_start: 0.7555 (t80) cc_final: 0.6303 (t80) REVERT: D 265 ARG cc_start: 0.8016 (ttm110) cc_final: 0.7764 (ttm170) REVERT: E 14 LYS cc_start: 0.8208 (mmmt) cc_final: 0.7931 (mmmt) REVERT: E 19 MET cc_start: 0.7904 (mmt) cc_final: 0.7531 (mmt) REVERT: E 95 MET cc_start: 0.7596 (mtm) cc_final: 0.7369 (mtm) REVERT: E 155 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8584 (mmtm) REVERT: F 91 MET cc_start: 0.7627 (mmt) cc_final: 0.7260 (mmm) REVERT: F 95 MET cc_start: 0.5279 (mmp) cc_final: 0.4742 (mmp) REVERT: F 115 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8330 (m) REVERT: F 163 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6369 (tm-30) REVERT: G 86 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7451 (t80) REVERT: H 12 ASN cc_start: 0.6702 (p0) cc_final: 0.6402 (p0) REVERT: H 16 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7132 (mp) REVERT: H 18 LYS cc_start: 0.7579 (mppt) cc_final: 0.7107 (mmmm) REVERT: H 82 MET cc_start: 0.8013 (tpt) cc_final: 0.7808 (tpt) REVERT: H 83 GLU cc_start: 0.6865 (pp20) cc_final: 0.6516 (pp20) REVERT: H 119 MET cc_start: 0.4722 (ptt) cc_final: 0.3996 (ptt) REVERT: H 276 GLU cc_start: 0.7049 (tp30) cc_final: 0.6596 (tp30) REVERT: H 334 GLU cc_start: 0.6564 (mp0) cc_final: 0.5870 (mp0) REVERT: I 16 LEU cc_start: 0.6634 (tt) cc_final: 0.6031 (mt) REVERT: I 107 GLU cc_start: 0.6501 (pm20) cc_final: 0.5739 (pm20) REVERT: I 123 MET cc_start: 0.6636 (mmp) cc_final: 0.6411 (mmp) REVERT: I 214 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7505 (mt-10) REVERT: I 238 LYS cc_start: 0.6626 (mttp) cc_final: 0.6369 (mtmm) REVERT: I 259 GLU cc_start: 0.6981 (tp30) cc_final: 0.6274 (tp30) REVERT: I 316 GLU cc_start: 0.7726 (tt0) cc_final: 0.7419 (tt0) REVERT: N 176 MET cc_start: 0.6922 (mtp) cc_final: 0.6509 (mtt) REVERT: N 191 LYS cc_start: 0.7310 (tptt) cc_final: 0.7071 (tppt) REVERT: N 282 ILE cc_start: 0.7267 (tt) cc_final: 0.7006 (pt) REVERT: O 190 MET cc_start: 0.6932 (ttm) cc_final: 0.6598 (ttp) REVERT: O 195 GLU cc_start: 0.7466 (pt0) cc_final: 0.7252 (pt0) REVERT: O 227 MET cc_start: 0.7748 (mmm) cc_final: 0.7418 (mmm) REVERT: O 328 LYS cc_start: 0.7277 (tptt) cc_final: 0.7054 (tptt) REVERT: P 91 TYR cc_start: 0.8008 (m-80) cc_final: 0.7766 (m-80) REVERT: P 111 ASN cc_start: 0.7305 (m-40) cc_final: 0.7003 (m-40) REVERT: P 155 SER cc_start: 0.7771 (p) cc_final: 0.7512 (p) REVERT: P 177 ARG cc_start: 0.7817 (ttt-90) cc_final: 0.7156 (ttt-90) REVERT: P 211 ASP cc_start: 0.7596 (t70) cc_final: 0.7320 (t70) REVERT: P 214 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6816 (mt-10) REVERT: P 226 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6690 (mm-30) REVERT: P 352 PHE cc_start: 0.7361 (t80) cc_final: 0.7139 (t80) REVERT: P 356 TRP cc_start: 0.8237 (m100) cc_final: 0.7527 (m100) REVERT: Q 68 LYS cc_start: 0.8137 (mtmm) cc_final: 0.7887 (mtpp) REVERT: Q 132 MET cc_start: 0.6279 (ppp) cc_final: 0.6046 (tmm) REVERT: Q 171 LEU cc_start: 0.8034 (mm) cc_final: 0.7788 (mp) REVERT: Q 190 MET cc_start: 0.6557 (mtt) cc_final: 0.6329 (mtp) REVERT: Q 207 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6785 (mm-30) REVERT: Q 210 ARG cc_start: 0.7410 (ttm-80) cc_final: 0.7017 (ttm-80) REVERT: Q 214 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6299 (tt0) REVERT: Q 255 PHE cc_start: 0.6459 (p90) cc_final: 0.6245 (p90) REVERT: Q 300 SER cc_start: 0.7844 (m) cc_final: 0.7640 (p) REVERT: Q 325 MET cc_start: 0.7719 (pmm) cc_final: 0.6059 (ptt) REVERT: R 47 MET cc_start: 0.4147 (mpp) cc_final: 0.3931 (mmm) REVERT: R 82 MET cc_start: 0.7464 (mmm) cc_final: 0.7202 (tpt) REVERT: R 121 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7455 (tm-30) REVERT: R 151 ILE cc_start: 0.7982 (tp) cc_final: 0.7692 (pt) REVERT: R 176 MET cc_start: 0.7382 (mtt) cc_final: 0.7102 (mtp) REVERT: R 248 ILE cc_start: 0.8577 (mm) cc_final: 0.8023 (tt) REVERT: R 334 GLU cc_start: 0.7574 (pm20) cc_final: 0.7163 (pm20) REVERT: R 346 LEU cc_start: 0.7790 (tt) cc_final: 0.7543 (tt) REVERT: R 359 LYS cc_start: 0.7779 (tttp) cc_final: 0.7554 (tttp) REVERT: S 66 THR cc_start: 0.7277 (m) cc_final: 0.7006 (p) REVERT: S 120 THR cc_start: 0.7445 (m) cc_final: 0.7080 (t) REVERT: S 283 MET cc_start: 0.7036 (mmm) cc_final: 0.6510 (mmm) REVERT: S 334 GLU cc_start: 0.6018 (pm20) cc_final: 0.5791 (pm20) REVERT: S 352 PHE cc_start: 0.4598 (t80) cc_final: 0.4300 (t80) REVERT: i 1 TRP cc_start: 0.8014 (m100) cc_final: 0.7442 (m100) outliers start: 82 outliers final: 47 residues processed: 1222 average time/residue: 0.6242 time to fit residues: 1278.8029 Evaluate side-chains 1194 residues out of total 6097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 1143 time to evaluate : 5.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 269 HIS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 313 MET Chi-restraints excluded: chain O residue 44 MET Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 194 THR Chi-restraints excluded: chain P residue 373 LYS Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 248 ILE Chi-restraints excluded: chain Q residue 326 LYS Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 300 SER Chi-restraints excluded: chain R residue 351 THR Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 368 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 356 optimal weight: 0.8980 chunk 199 optimal weight: 0.0270 chunk 534 optimal weight: 1.9990 chunk 437 optimal weight: 0.0470 chunk 177 optimal weight: 0.0040 chunk 643 optimal weight: 8.9990 chunk 694 optimal weight: 8.9990 chunk 572 optimal weight: 0.5980 chunk 637 optimal weight: 0.4980 chunk 219 optimal weight: 0.1980 chunk 515 optimal weight: 0.5980 overall best weight: 0.1548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 269 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 ASN F 120 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 ASN H 121 GLN O 87 HIS O 92 ASN ** P 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 173 HIS R 111 ASN R 173 HIS S 40 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 51616 Z= 0.156 Angle : 0.615 10.342 70401 Z= 0.300 Chirality : 0.045 0.279 8177 Planarity : 0.003 0.044 9210 Dihedral : 9.171 169.053 8007 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.70 % Allowed : 14.00 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.10), residues: 7041 helix: 1.74 (0.10), residues: 2624 sheet: 0.72 (0.17), residues: 1080 loop : -0.19 (0.11), residues: 3337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 79 HIS 0.016 0.001 HIS P 275 PHE 0.025 0.001 PHE A 292 TYR 0.024 0.001 TYR D 43 ARG 0.006 0.000 ARG F 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14082 Ramachandran restraints generated. 7041 Oldfield, 0 Emsley, 7041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14082 Ramachandran restraints generated. 7041 Oldfield, 0 Emsley, 7041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 6097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1164 time to evaluate : 5.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6164 (mp10) REVERT: A 94 GLU cc_start: 0.7548 (pt0) cc_final: 0.7167 (tt0) REVERT: A 99 LYS cc_start: 0.7449 (mtpp) cc_final: 0.6951 (mtmm) REVERT: A 114 GLU cc_start: 0.7396 (pm20) cc_final: 0.7160 (pm20) REVERT: A 130 MET cc_start: 0.6879 (mmm) cc_final: 0.6638 (tpp) REVERT: A 135 ASN cc_start: 0.7845 (m110) cc_final: 0.7569 (m-40) REVERT: A 294 GLN cc_start: 0.7551 (tp40) cc_final: 0.7301 (tt0) REVERT: B 86 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7843 (ttpp) REVERT: B 106 LYS cc_start: 0.8270 (mmtm) cc_final: 0.7910 (mmmt) REVERT: B 146 LEU cc_start: 0.7274 (mp) cc_final: 0.6871 (mt) REVERT: B 158 ASP cc_start: 0.7130 (t0) cc_final: 0.6799 (t0) REVERT: B 226 ASN cc_start: 0.8122 (t0) cc_final: 0.7814 (t0) REVERT: B 263 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6412 (tp30) REVERT: B 328 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.6658 (mtm-85) REVERT: C 42 TRP cc_start: 0.7875 (m100) cc_final: 0.7021 (m100) REVERT: C 94 ARG cc_start: 0.7261 (mtt180) cc_final: 0.6907 (mtt180) REVERT: C 95 ILE cc_start: 0.7827 (mm) cc_final: 0.7617 (mm) REVERT: C 104 TRP cc_start: 0.7435 (m100) cc_final: 0.6607 (m100) REVERT: C 108 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6709 (mm-30) REVERT: C 148 LEU cc_start: 0.8100 (mp) cc_final: 0.7884 (mt) REVERT: C 163 ASP cc_start: 0.6131 (p0) cc_final: 0.5797 (p0) REVERT: C 254 THR cc_start: 0.7951 (t) cc_final: 0.7630 (m) REVERT: C 300 GLU cc_start: 0.5448 (tm-30) cc_final: 0.5105 (tm-30) REVERT: C 301 ARG cc_start: 0.7817 (ttm-80) cc_final: 0.7326 (ttm-80) REVERT: C 335 LEU cc_start: 0.6869 (mm) cc_final: 0.6647 (mm) REVERT: C 336 SER cc_start: 0.7165 (m) cc_final: 0.6943 (p) REVERT: D 158 LYS cc_start: 0.7239 (tppt) cc_final: 0.7009 (mmmt) REVERT: D 263 HIS cc_start: 0.8217 (m170) cc_final: 0.8000 (m-70) REVERT: E 14 LYS cc_start: 0.8210 (mmmt) cc_final: 0.7901 (mmmt) REVERT: E 93 LYS cc_start: 0.8413 (mmmt) cc_final: 0.8050 (mptp) REVERT: E 95 MET cc_start: 0.7562 (mtm) cc_final: 0.7321 (mtm) REVERT: E 155 LYS cc_start: 0.9045 (mmtt) cc_final: 0.8542 (mmtt) REVERT: F 115 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8364 (m) REVERT: F 163 GLU cc_start: 0.6705 (tm-30) cc_final: 0.6457 (tm-30) REVERT: G 86 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7620 (t80) REVERT: H 12 ASN cc_start: 0.6755 (p0) cc_final: 0.6342 (p0) REVERT: H 71 ILE cc_start: 0.5619 (OUTLIER) cc_final: 0.5370 (pt) REVERT: H 83 GLU cc_start: 0.6857 (pp20) cc_final: 0.6519 (pp20) REVERT: H 276 GLU cc_start: 0.6941 (tp30) cc_final: 0.6138 (tm-30) REVERT: I 72 GLU cc_start: 0.6889 (pt0) cc_final: 0.6115 (pp20) REVERT: I 82 MET cc_start: 0.6048 (tpp) cc_final: 0.5296 (tpp) REVERT: I 100 GLU cc_start: 0.7770 (tp30) cc_final: 0.7311 (tp30) REVERT: I 107 GLU cc_start: 0.6583 (pm20) cc_final: 0.5765 (pm20) REVERT: I 121 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7706 (tm-30) REVERT: I 214 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7445 (mt-10) REVERT: I 259 GLU cc_start: 0.6896 (tp30) cc_final: 0.6037 (tp30) REVERT: N 176 MET cc_start: 0.6726 (mtp) cc_final: 0.6411 (mtt) REVERT: N 191 LYS cc_start: 0.7461 (tptt) cc_final: 0.7136 (tppt) REVERT: N 238 LYS cc_start: 0.7369 (mmtm) cc_final: 0.7028 (mmtm) REVERT: N 282 ILE cc_start: 0.7290 (tt) cc_final: 0.6976 (pt) REVERT: O 121 GLN cc_start: 0.6867 (pt0) cc_final: 0.6663 (pt0) REVERT: O 190 MET cc_start: 0.6906 (ttm) cc_final: 0.6634 (ttp) REVERT: O 195 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7063 (pt0) REVERT: O 227 MET cc_start: 0.7746 (mmm) cc_final: 0.7409 (mmm) REVERT: O 255 PHE cc_start: 0.7494 (p90) cc_final: 0.6922 (p90) REVERT: P 91 TYR cc_start: 0.7914 (m-80) cc_final: 0.7642 (m-80) REVERT: P 111 ASN cc_start: 0.7441 (m-40) cc_final: 0.6999 (m-40) REVERT: P 176 MET cc_start: 0.7036 (mtp) cc_final: 0.6595 (mmm) REVERT: P 214 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6674 (mt-10) REVERT: P 226 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6719 (mm-30) REVERT: P 294 TYR cc_start: 0.7405 (m-80) cc_final: 0.6997 (m-80) REVERT: Q 72 GLU cc_start: 0.5691 (tm-30) cc_final: 0.5106 (tm-30) REVERT: Q 171 LEU cc_start: 0.8061 (mm) cc_final: 0.7728 (mp) REVERT: Q 190 MET cc_start: 0.6624 (mtt) cc_final: 0.6337 (mtp) REVERT: Q 255 PHE cc_start: 0.6453 (p90) cc_final: 0.6252 (p90) REVERT: Q 305 MET cc_start: 0.7034 (mmm) cc_final: 0.6736 (mmm) REVERT: Q 313 MET cc_start: 0.6129 (tpp) cc_final: 0.5756 (tpp) REVERT: Q 325 MET cc_start: 0.7782 (pmm) cc_final: 0.5727 (ptp) REVERT: Q 335 ARG cc_start: 0.7068 (mtm110) cc_final: 0.6832 (mtm180) REVERT: Q 360 GLN cc_start: 0.6757 (tp40) cc_final: 0.6468 (tp40) REVERT: R 210 ARG cc_start: 0.7604 (tmm-80) cc_final: 0.6860 (ttp80) REVERT: R 248 ILE cc_start: 0.8553 (mm) cc_final: 0.8013 (tt) REVERT: R 259 GLU cc_start: 0.6632 (tm-30) cc_final: 0.6354 (tm-30) REVERT: R 346 LEU cc_start: 0.7759 (tt) cc_final: 0.7523 (tt) REVERT: S 47 MET cc_start: 0.2431 (mmm) cc_final: 0.2071 (mmm) REVERT: S 66 THR cc_start: 0.7293 (m) cc_final: 0.7071 (p) REVERT: S 120 THR cc_start: 0.7444 (m) cc_final: 0.7072 (t) REVERT: S 195 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6313 (pt0) REVERT: i 1 TRP cc_start: 0.8152 (m100) cc_final: 0.7892 (m100) outliers start: 113 outliers final: 65 residues processed: 1205 average time/residue: 0.6086 time to fit residues: 1222.5650 Evaluate side-chains 1190 residues out of total 6097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 1119 time to evaluate : 5.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain N residue 90 PHE Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 313 MET Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 201 VAL Chi-restraints excluded: chain O residue 293 LEU Chi-restraints excluded: chain O residue 358 THR Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 305 MET Chi-restraints excluded: chain P residue 330 ILE Chi-restraints excluded: chain P residue 373 LYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 303 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain S residue 14 SER Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain S residue 368 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 635 optimal weight: 8.9990 chunk 483 optimal weight: 0.5980 chunk 333 optimal weight: 30.0000 chunk 71 optimal weight: 0.5980 chunk 306 optimal weight: 10.0000 chunk 431 optimal weight: 0.7980 chunk 645 optimal weight: 40.0000 chunk 683 optimal weight: 40.0000 chunk 337 optimal weight: 8.9990 chunk 611 optimal weight: 3.9990 chunk 184 optimal weight: 0.3980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 205 GLN B 26 ASN B 165 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 ASN ** H 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 360 GLN ** N 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 87 HIS P 12 ASN P 121 GLN ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 88 HIS ** R 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 HIS R 296 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 51616 Z= 0.289 Angle : 0.694 9.860 70401 Z= 0.348 Chirality : 0.049 0.260 8177 Planarity : 0.004 0.056 9210 Dihedral : 8.836 160.354 8007 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.84 % Favored : 95.14 % Rotamer: Outliers : 3.51 % Allowed : 15.62 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.10), residues: 7041 helix: 1.36 (0.10), residues: 2681 sheet: 0.38 (0.16), residues: 1039 loop : -0.46 (0.11), residues: 3321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 79 HIS 0.030 0.002 HIS P 275 PHE 0.030 0.002 PHE C 252 TYR 0.026 0.002 TYR D 43 ARG 0.028 0.001 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14082 Ramachandran restraints generated. 7041 Oldfield, 0 Emsley, 7041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14082 Ramachandran restraints generated. 7041 Oldfield, 0 Emsley, 7041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1366 residues out of total 6097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1219 time to evaluate : 5.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6581 (tp30) REVERT: A 114 GLU cc_start: 0.7503 (pm20) cc_final: 0.7248 (pm20) REVERT: A 130 MET cc_start: 0.7424 (mmm) cc_final: 0.7112 (tpp) REVERT: A 135 ASN cc_start: 0.7906 (m110) cc_final: 0.7625 (m-40) REVERT: A 182 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7344 (mm-30) REVERT: A 206 GLN cc_start: 0.7857 (tp40) cc_final: 0.7431 (tm-30) REVERT: A 305 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7406 (mm-40) REVERT: B 40 ILE cc_start: 0.8121 (tp) cc_final: 0.7860 (tp) REVERT: B 86 LYS cc_start: 0.8317 (ttpp) cc_final: 0.8016 (ttpp) REVERT: B 106 LYS cc_start: 0.8371 (mmtm) cc_final: 0.8058 (mmmt) REVERT: B 145 THR cc_start: 0.7142 (p) cc_final: 0.6890 (p) REVERT: B 146 LEU cc_start: 0.7545 (mp) cc_final: 0.7023 (mp) REVERT: B 158 ASP cc_start: 0.7316 (t0) cc_final: 0.7067 (t0) REVERT: B 226 ASN cc_start: 0.8327 (t0) cc_final: 0.7927 (t0) REVERT: B 263 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6568 (tp30) REVERT: B 309 MET cc_start: 0.7605 (tpp) cc_final: 0.7321 (tpt) REVERT: C 3 TYR cc_start: 0.8161 (t80) cc_final: 0.7901 (t80) REVERT: C 13 CYS cc_start: 0.6939 (t) cc_final: 0.6488 (t) REVERT: C 42 TRP cc_start: 0.7956 (m100) cc_final: 0.7283 (m100) REVERT: C 95 ILE cc_start: 0.8141 (mm) cc_final: 0.7823 (mm) REVERT: C 104 TRP cc_start: 0.7509 (m100) cc_final: 0.6253 (m100) REVERT: C 108 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6482 (mm-30) REVERT: C 145 VAL cc_start: 0.7699 (OUTLIER) cc_final: 0.7494 (t) REVERT: C 161 SER cc_start: 0.8347 (t) cc_final: 0.8120 (t) REVERT: C 162 CYS cc_start: 0.7583 (p) cc_final: 0.7241 (p) REVERT: C 254 THR cc_start: 0.7831 (t) cc_final: 0.7568 (m) REVERT: C 300 GLU cc_start: 0.5820 (tm-30) cc_final: 0.5441 (tm-30) REVERT: C 301 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7485 (ttm-80) REVERT: C 335 LEU cc_start: 0.7392 (mm) cc_final: 0.7003 (mm) REVERT: C 336 SER cc_start: 0.7406 (m) cc_final: 0.7126 (p) REVERT: D 119 ASN cc_start: 0.7161 (t0) cc_final: 0.6895 (t0) REVERT: D 158 LYS cc_start: 0.7255 (tppt) cc_final: 0.7001 (mmmt) REVERT: E 93 LYS cc_start: 0.8462 (mmmt) cc_final: 0.8179 (mttm) REVERT: E 95 MET cc_start: 0.7742 (mtm) cc_final: 0.7525 (mtm) REVERT: E 155 LYS cc_start: 0.9070 (mmtt) cc_final: 0.8634 (mmtm) REVERT: F 44 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8268 (mmtt) REVERT: F 91 MET cc_start: 0.8257 (mmm) cc_final: 0.7207 (mmm) REVERT: F 95 MET cc_start: 0.5571 (mmp) cc_final: 0.5157 (mmp) REVERT: F 115 SER cc_start: 0.8680 (p) cc_final: 0.8413 (m) REVERT: F 144 LYS cc_start: 0.7762 (mmmm) cc_final: 0.7535 (mmmm) REVERT: F 163 GLU cc_start: 0.6700 (tm-30) cc_final: 0.6341 (tm-30) REVERT: G 86 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7589 (t80) REVERT: G 108 LYS cc_start: 0.8208 (mttp) cc_final: 0.7749 (tttp) REVERT: H 12 ASN cc_start: 0.6958 (p0) cc_final: 0.6573 (p0) REVERT: H 18 LYS cc_start: 0.7496 (mppt) cc_final: 0.7085 (mppt) REVERT: H 83 GLU cc_start: 0.7139 (pp20) cc_final: 0.6813 (pp20) REVERT: H 276 GLU cc_start: 0.7523 (tp30) cc_final: 0.6265 (tm-30) REVERT: H 314 GLN cc_start: 0.7243 (tm-30) cc_final: 0.6770 (tm-30) REVERT: H 334 GLU cc_start: 0.7063 (mp0) cc_final: 0.6626 (mp0) REVERT: I 72 GLU cc_start: 0.6840 (pt0) cc_final: 0.5804 (pp20) REVERT: I 82 MET cc_start: 0.6060 (tpp) cc_final: 0.5364 (tpp) REVERT: I 107 GLU cc_start: 0.6947 (pm20) cc_final: 0.6092 (pm20) REVERT: I 121 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7642 (tm-30) REVERT: I 189 LEU cc_start: 0.7517 (tp) cc_final: 0.7247 (tp) REVERT: I 215 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8361 (ttmm) REVERT: I 247 VAL cc_start: 0.8409 (t) cc_final: 0.8137 (p) REVERT: I 316 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7150 (tp30) REVERT: N 12 ASN cc_start: 0.5672 (m-40) cc_final: 0.5459 (m110) REVERT: N 120 THR cc_start: 0.7855 (m) cc_final: 0.7602 (t) REVERT: N 176 MET cc_start: 0.7143 (mtp) cc_final: 0.6849 (mtm) REVERT: N 191 LYS cc_start: 0.7420 (tptt) cc_final: 0.6918 (tppt) REVERT: N 238 LYS cc_start: 0.7503 (mmtm) cc_final: 0.6744 (mppt) REVERT: N 282 ILE cc_start: 0.7376 (tt) cc_final: 0.7069 (pt) REVERT: O 121 GLN cc_start: 0.7027 (pt0) cc_final: 0.6809 (pt0) REVERT: O 195 GLU cc_start: 0.7498 (pt0) cc_final: 0.7139 (pt0) REVERT: O 227 MET cc_start: 0.7967 (mmm) cc_final: 0.7531 (mmm) REVERT: O 288 ASP cc_start: 0.5846 (OUTLIER) cc_final: 0.5424 (t0) REVERT: P 31 PHE cc_start: 0.8358 (p90) cc_final: 0.8073 (p90) REVERT: P 66 THR cc_start: 0.8130 (p) cc_final: 0.7775 (t) REVERT: P 111 ASN cc_start: 0.7424 (m-40) cc_final: 0.7104 (m-40) REVERT: P 176 MET cc_start: 0.6899 (mtp) cc_final: 0.6463 (mmm) REVERT: P 195 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6323 (pt0) REVERT: P 214 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7095 (mt-10) REVERT: P 313 MET cc_start: 0.6389 (mmm) cc_final: 0.5643 (tmm) REVERT: Q 190 MET cc_start: 0.6730 (mtt) cc_final: 0.6422 (mtp) REVERT: Q 214 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6548 (tt0) REVERT: Q 255 PHE cc_start: 0.6617 (p90) cc_final: 0.6312 (p90) REVERT: Q 305 MET cc_start: 0.7132 (mmm) cc_final: 0.6736 (mmm) REVERT: Q 325 MET cc_start: 0.7913 (pmm) cc_final: 0.5747 (ptp) REVERT: Q 335 ARG cc_start: 0.7372 (mtm110) cc_final: 0.6460 (mtm180) REVERT: Q 360 GLN cc_start: 0.7162 (tp40) cc_final: 0.6832 (tp40) REVERT: R 85 ILE cc_start: 0.8132 (tt) cc_final: 0.7797 (tp) REVERT: R 121 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7578 (tm-30) REVERT: R 176 MET cc_start: 0.7426 (mtt) cc_final: 0.7107 (mtp) REVERT: R 177 ARG cc_start: 0.7755 (ttt-90) cc_final: 0.7431 (ttt-90) REVERT: R 248 ILE cc_start: 0.8497 (mm) cc_final: 0.7684 (tt) REVERT: R 250 ILE cc_start: 0.6913 (mm) cc_final: 0.6551 (mm) REVERT: R 318 THR cc_start: 0.8133 (m) cc_final: 0.7900 (t) REVERT: R 356 TRP cc_start: 0.8802 (m100) cc_final: 0.7804 (m100) REVERT: S 47 MET cc_start: 0.2774 (mmm) cc_final: 0.2351 (mmm) REVERT: S 66 THR cc_start: 0.7495 (m) cc_final: 0.7103 (p) REVERT: S 120 THR cc_start: 0.7481 (m) cc_final: 0.7143 (t) REVERT: S 152 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7835 (m) REVERT: S 219 VAL cc_start: 0.7606 (p) cc_final: 0.6742 (t) REVERT: S 222 ASP cc_start: 0.6915 (t70) cc_final: 0.6471 (t70) REVERT: S 248 ILE cc_start: 0.6312 (OUTLIER) cc_final: 0.6056 (pp) REVERT: S 283 MET cc_start: 0.6950 (mmm) cc_final: 0.6562 (mmm) outliers start: 147 outliers final: 87 residues processed: 1279 average time/residue: 0.6177 time to fit residues: 1308.2056 Evaluate side-chains 1293 residues out of total 6097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 1200 time to evaluate : 5.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 31 PHE Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 303 THR Chi-restraints excluded: chain N residue 313 MET Chi-restraints excluded: chain N residue 316 GLU Chi-restraints excluded: chain N residue 330 ILE Chi-restraints excluded: chain O residue 44 MET Chi-restraints excluded: chain O residue 142 LEU Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 201 VAL Chi-restraints excluded: chain O residue 260 THR Chi-restraints excluded: chain O residue 288 ASP Chi-restraints excluded: chain P residue 12 ASN Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 165 ILE Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 194 THR Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 299 MET Chi-restraints excluded: chain P residue 330 ILE Chi-restraints excluded: chain P residue 373 LYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 248 ILE Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 326 LYS Chi-restraints excluded: chain R residue 44 MET Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 218 TYR Chi-restraints excluded: chain R residue 300 SER Chi-restraints excluded: chain R residue 351 THR Chi-restraints excluded: chain R residue 364 GLU Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 232 SER Chi-restraints excluded: chain S residue 248 ILE Chi-restraints excluded: chain S residue 298 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 569 optimal weight: 0.3980 chunk 387 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 508 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 chunk 583 optimal weight: 0.1980 chunk 472 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 348 optimal weight: 1.9990 chunk 613 optimal weight: 0.1980 chunk 172 optimal weight: 3.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: