Starting phenix.real_space_refine on Sun Feb 25 11:16:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpt_26063/02_2024/7tpt_26063_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpt_26063/02_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_26063/02_2024/7tpt_26063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpt_26063/02_2024/7tpt_26063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpt_26063/02_2024/7tpt_26063_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpt_26063/02_2024/7tpt_26063_updated.pdb" } 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 Residue "C GLU 363": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 50755 Number of models: 1 Model: "" Number of chains: 52 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: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "b" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "c" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "d" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "e" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "f" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "g" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "h" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "i" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "j" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "k" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "l" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "m" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "n" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "o" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 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: 25.62, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.82 Conformation dependent library (CDL) restraints added in 9.3 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... running ksdssp... Secondary structure from input PDB file: 330 helices and 89 sheets defined 40.2% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.53 Creating SS restraints... Processing helix chain 'A' and resid 54 through 58 removed outlier: 4.254A pdb=" N ASP A 57 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 87 through 99 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.662A pdb=" N TRP A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N THR A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.918A pdb=" N ASP A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 removed outlier: 4.641A pdb=" N LEU A 221 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLU A 222 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 225 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 226 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 273 through 282 removed outlier: 3.881A pdb=" N LEU A 277 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLY A 278 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 309 through 317 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) No H-bonds generated for 'chain 'A' and resid 309 through 317' Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.560A pdb=" N LEU A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 386 Processing helix chain 'A' and resid 388 through 393 removed outlier: 3.717A pdb=" N GLN A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.794A pdb=" N GLU A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'B' and resid 59 through 67 removed outlier: 3.535A pdb=" N GLU B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N MET B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 141 through 148 removed outlier: 4.811A pdb=" N ALA B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 209 through 219 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 227 through 236 Processing helix chain 'B' and resid 257 through 260 No H-bonds generated for 'chain 'B' and resid 257 through 260' Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 268 through 271 Processing helix chain 'B' and resid 278 through 288 Processing helix chain 'B' and resid 292 through 299 removed outlier: 4.474A pdb=" N GLU B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 313 through 328 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 354 through 364 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 298 through 307 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 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'D' and resid 9 through 21 removed outlier: 4.053A pdb=" N ASN D 21 " --> pdb=" O LEU D 17 " (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 64 through 70 Processing helix chain 'D' and resid 107 through 114 Processing helix chain 'D' and resid 116 through 134 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) Processing helix chain 'D' and resid 172 through 183 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) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 through 231' Processing helix chain 'D' and resid 237 through 280 removed outlier: 4.723A pdb=" N ARG D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASP D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) 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) removed outlier: 4.055A pdb=" N ARG D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ALA D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 52 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) Processing helix chain 'E' and resid 63 through 82 Processing helix chain 'E' and resid 88 through 99 Processing helix chain 'E' and resid 123 through 148 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) Processing helix chain 'E' and resid 158 through 164 removed outlier: 5.042A pdb=" N PHE E 163 " --> pdb=" O TRP E 159 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL E 164 " --> pdb=" O TRP E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'F' and resid 6 through 19 Processing helix chain 'F' and resid 37 through 40 No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 81 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 129 through 165 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 40 through 48 Processing helix chain 'G' and resid 51 through 59 Processing helix chain 'G' and resid 69 through 84 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 100 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 123 through 135 Processing helix chain 'G' and resid 138 through 145 Processing helix chain 'H' and resid 57 through 60 No H-bonds generated for 'chain 'H' and resid 57 through 60' Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 137 through 145 Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 182 through 196 Processing helix chain 'H' and resid 203 through 215 Processing helix chain 'H' and resid 223 through 231 Processing helix chain 'H' and resid 252 through 256 removed outlier: 3.508A pdb=" N ARG H 256 " --> pdb=" O GLU H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 262 Processing helix chain 'H' and resid 264 through 266 No H-bonds generated for 'chain 'H' and resid 264 through 266' Processing helix chain 'H' and resid 274 through 284 Processing helix chain 'H' and resid 287 through 295 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 309 through 320 Processing helix chain 'H' and resid 335 through 348 removed outlier: 4.972A pdb=" N VAL H 339 " --> pdb=" O LYS H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 354 removed outlier: 3.855A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 351 through 354' Processing helix chain 'H' and resid 359 through 365 Processing helix chain 'H' and resid 367 through 372 removed outlier: 3.510A pdb=" N VAL H 370 " --> pdb=" O PRO H 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 79 through 91 Processing helix chain 'I' and resid 113 through 125 Processing helix chain 'I' and resid 137 through 145 Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 182 through 196 Processing helix chain 'I' and resid 203 through 215 Processing helix chain 'I' and resid 223 through 231 Processing helix chain 'I' and resid 252 through 256 removed outlier: 3.508A pdb=" N ARG I 256 " --> pdb=" O GLU I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 262 Processing helix chain 'I' and resid 264 through 266 No H-bonds generated for 'chain 'I' and resid 264 through 266' Processing helix chain 'I' and resid 274 through 284 Processing helix chain 'I' and resid 287 through 295 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 309 through 320 Processing helix chain 'I' and resid 335 through 348 removed outlier: 4.972A pdb=" N VAL I 339 " --> pdb=" O LYS I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 354 removed outlier: 3.855A pdb=" N GLN I 354 " --> pdb=" O THR I 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 351 through 354' Processing helix chain 'I' and resid 359 through 365 Processing helix chain 'I' and resid 367 through 372 removed outlier: 3.511A pdb=" N VAL I 370 " --> pdb=" O PRO I 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'J' and resid 79 through 91 Processing helix chain 'J' and resid 113 through 125 Processing helix chain 'J' and resid 137 through 145 Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 182 through 196 Processing helix chain 'J' and resid 203 through 215 Processing helix chain 'J' and resid 223 through 231 Processing helix chain 'J' and resid 252 through 256 removed outlier: 3.508A pdb=" N ARG J 256 " --> pdb=" O GLU J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 262 Processing helix chain 'J' and resid 264 through 266 No H-bonds generated for 'chain 'J' and resid 264 through 266' Processing helix chain 'J' and resid 274 through 284 Processing helix chain 'J' and resid 287 through 295 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 309 through 320 Processing helix chain 'J' and resid 335 through 348 removed outlier: 4.972A pdb=" N VAL J 339 " --> pdb=" O LYS J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 354 removed outlier: 3.855A pdb=" N GLN J 354 " --> pdb=" O THR J 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 351 through 354' Processing helix chain 'J' and resid 359 through 365 Processing helix chain 'J' and resid 367 through 372 removed outlier: 3.510A pdb=" N VAL J 370 " --> pdb=" O PRO J 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 60 Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 79 through 91 Processing helix chain 'K' and resid 113 through 125 Processing helix chain 'K' and resid 137 through 145 Processing helix chain 'K' and resid 172 through 174 No H-bonds generated for 'chain 'K' and resid 172 through 174' Processing helix chain 'K' and resid 182 through 196 Processing helix chain 'K' and resid 203 through 215 Processing helix chain 'K' and resid 223 through 231 Processing helix chain 'K' and resid 252 through 256 removed outlier: 3.507A pdb=" N ARG K 256 " --> pdb=" O GLU K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 262 Processing helix chain 'K' and resid 264 through 266 No H-bonds generated for 'chain 'K' and resid 264 through 266' Processing helix chain 'K' and resid 274 through 284 Processing helix chain 'K' and resid 287 through 295 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 309 through 320 Processing helix chain 'K' and resid 335 through 348 removed outlier: 4.972A pdb=" N VAL K 339 " --> pdb=" O LYS K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 354 removed outlier: 3.856A pdb=" N GLN K 354 " --> pdb=" O THR K 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 351 through 354' Processing helix chain 'K' and resid 359 through 365 Processing helix chain 'K' and resid 367 through 372 removed outlier: 3.510A pdb=" N VAL K 370 " --> pdb=" O PRO K 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 60 Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 79 through 91 Processing helix chain 'L' and resid 113 through 125 Processing helix chain 'L' and resid 137 through 145 Processing helix chain 'L' and resid 172 through 174 No H-bonds generated for 'chain 'L' and resid 172 through 174' Processing helix chain 'L' and resid 182 through 196 Processing helix chain 'L' and resid 203 through 215 Processing helix chain 'L' and resid 223 through 231 Processing helix chain 'L' and resid 252 through 256 removed outlier: 3.508A pdb=" N ARG L 256 " --> pdb=" O GLU L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 262 Processing helix chain 'L' and resid 264 through 266 No H-bonds generated for 'chain 'L' and resid 264 through 266' Processing helix chain 'L' and resid 274 through 284 Processing helix chain 'L' and resid 287 through 295 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 309 through 320 Processing helix chain 'L' and resid 335 through 348 removed outlier: 4.972A pdb=" N VAL L 339 " --> pdb=" O LYS L 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 354 removed outlier: 3.855A pdb=" N GLN L 354 " --> pdb=" O THR L 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 351 through 354' Processing helix chain 'L' and resid 359 through 365 Processing helix chain 'L' and resid 367 through 372 removed outlier: 3.511A pdb=" N VAL L 370 " --> pdb=" O PRO L 367 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 60 Processing helix chain 'M' and resid 62 through 64 No H-bonds generated for 'chain 'M' and resid 62 through 64' Processing helix chain 'M' and resid 79 through 91 Processing helix chain 'M' and resid 113 through 125 Processing helix chain 'M' and resid 137 through 145 Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 182 through 196 Processing helix chain 'M' and resid 203 through 215 Processing helix chain 'M' and resid 223 through 231 Processing helix chain 'M' and resid 252 through 256 removed outlier: 3.507A pdb=" N ARG M 256 " --> pdb=" O GLU M 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 262 Processing helix chain 'M' and resid 264 through 266 No H-bonds generated for 'chain 'M' and resid 264 through 266' Processing helix chain 'M' and resid 274 through 284 Processing helix chain 'M' and resid 287 through 295 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 309 through 320 Processing helix chain 'M' and resid 335 through 348 removed outlier: 4.972A pdb=" N VAL M 339 " --> pdb=" O LYS M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 354 removed outlier: 3.855A pdb=" N GLN M 354 " --> pdb=" O THR M 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 351 through 354' Processing helix chain 'M' and resid 359 through 365 Processing helix chain 'M' and resid 367 through 372 removed outlier: 3.511A pdb=" N VAL M 370 " --> pdb=" O PRO M 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 79 through 91 Processing helix chain 'N' and resid 113 through 125 Processing helix chain 'N' and resid 137 through 145 Processing helix chain 'N' and resid 172 through 174 No H-bonds generated for 'chain 'N' and resid 172 through 174' Processing helix chain 'N' and resid 182 through 196 Processing helix chain 'N' and resid 203 through 215 Processing helix chain 'N' and resid 223 through 231 Processing helix chain 'N' and resid 252 through 256 removed outlier: 3.507A pdb=" N ARG N 256 " --> pdb=" O GLU N 253 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 262 Processing helix chain 'N' and resid 264 through 266 No H-bonds generated for 'chain 'N' and resid 264 through 266' Processing helix chain 'N' and resid 274 through 284 Processing helix chain 'N' and resid 287 through 295 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 309 through 320 Processing helix chain 'N' and resid 335 through 348 removed outlier: 4.972A pdb=" N VAL N 339 " --> pdb=" O LYS N 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 351 through 354 removed outlier: 3.856A pdb=" N GLN N 354 " --> pdb=" O THR N 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 351 through 354' Processing helix chain 'N' and resid 359 through 365 Processing helix chain 'N' and resid 367 through 372 removed outlier: 3.510A pdb=" N VAL N 370 " --> pdb=" O PRO N 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 79 through 91 Processing helix chain 'O' and resid 113 through 125 Processing helix chain 'O' and resid 137 through 145 Processing helix chain 'O' and resid 172 through 174 No H-bonds generated for 'chain 'O' and resid 172 through 174' Processing helix chain 'O' and resid 182 through 196 Processing helix chain 'O' and resid 203 through 215 Processing helix chain 'O' and resid 223 through 231 Processing helix chain 'O' and resid 252 through 256 removed outlier: 3.508A pdb=" N ARG O 256 " --> pdb=" O GLU O 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 258 through 262 Processing helix chain 'O' and resid 264 through 266 No H-bonds generated for 'chain 'O' and resid 264 through 266' Processing helix chain 'O' and resid 274 through 284 Processing helix chain 'O' and resid 287 through 295 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 309 through 320 Processing helix chain 'O' and resid 335 through 348 removed outlier: 4.972A pdb=" N VAL O 339 " --> pdb=" O LYS O 336 " (cutoff:3.500A) Processing helix chain 'O' and resid 351 through 354 removed outlier: 3.856A pdb=" N GLN O 354 " --> pdb=" O THR O 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 351 through 354' Processing helix chain 'O' and resid 359 through 365 Processing helix chain 'O' and resid 367 through 372 removed outlier: 3.510A pdb=" N VAL O 370 " --> pdb=" O PRO O 367 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 60 Processing helix chain 'P' and resid 62 through 64 No H-bonds generated for 'chain 'P' and resid 62 through 64' Processing helix chain 'P' and resid 79 through 91 Processing helix chain 'P' and resid 113 through 125 Processing helix chain 'P' and resid 137 through 145 Processing helix chain 'P' and resid 172 through 174 No H-bonds generated for 'chain 'P' and resid 172 through 174' Processing helix chain 'P' and resid 182 through 196 Processing helix chain 'P' and resid 203 through 215 Processing helix chain 'P' and resid 223 through 231 Processing helix chain 'P' and resid 252 through 256 removed outlier: 3.508A pdb=" N ARG P 256 " --> pdb=" O GLU P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 258 through 262 Processing helix chain 'P' and resid 264 through 266 No H-bonds generated for 'chain 'P' and resid 264 through 266' Processing helix chain 'P' and resid 274 through 284 Processing helix chain 'P' and resid 287 through 295 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 309 through 320 Processing helix chain 'P' and resid 335 through 348 removed outlier: 4.972A pdb=" N VAL P 339 " --> pdb=" O LYS P 336 " (cutoff:3.500A) Processing helix chain 'P' and resid 351 through 354 removed outlier: 3.856A pdb=" N GLN P 354 " --> pdb=" O THR P 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 351 through 354' Processing helix chain 'P' and resid 359 through 364 Processing helix chain 'Q' and resid 55 through 60 Processing helix chain 'Q' and resid 62 through 64 No H-bonds generated for 'chain 'Q' and resid 62 through 64' Processing helix chain 'Q' and resid 79 through 91 Processing helix chain 'Q' and resid 113 through 125 Processing helix chain 'Q' and resid 137 through 145 Processing helix chain 'Q' and resid 172 through 174 No H-bonds generated for 'chain 'Q' and resid 172 through 174' Processing helix chain 'Q' and resid 182 through 196 Processing helix chain 'Q' and resid 203 through 215 Processing helix chain 'Q' and resid 223 through 231 Processing helix chain 'Q' and resid 252 through 256 removed outlier: 3.507A pdb=" N ARG Q 256 " --> pdb=" O GLU Q 253 " (cutoff:3.500A) Processing helix chain 'Q' and resid 258 through 262 Processing helix chain 'Q' and resid 264 through 266 No H-bonds generated for 'chain 'Q' and resid 264 through 266' Processing helix chain 'Q' and resid 274 through 284 Processing helix chain 'Q' and resid 287 through 295 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 309 through 320 Processing helix chain 'Q' and resid 335 through 348 removed outlier: 4.972A pdb=" N VAL Q 339 " --> pdb=" O LYS Q 336 " (cutoff:3.500A) Processing helix chain 'Q' and resid 351 through 354 removed outlier: 3.855A pdb=" N GLN Q 354 " --> pdb=" O THR Q 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 351 through 354' Processing helix chain 'Q' and resid 359 through 365 Processing helix chain 'Q' and resid 367 through 372 removed outlier: 3.510A pdb=" N VAL Q 370 " --> pdb=" O PRO Q 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 60 Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'R' and resid 79 through 91 Processing helix chain 'R' and resid 113 through 125 Processing helix chain 'R' and resid 137 through 145 Processing helix chain 'R' and resid 172 through 174 No H-bonds generated for 'chain 'R' and resid 172 through 174' Processing helix chain 'R' and resid 182 through 196 Processing helix chain 'R' and resid 203 through 215 Processing helix chain 'R' and resid 223 through 231 Processing helix chain 'R' and resid 252 through 256 removed outlier: 3.508A pdb=" N ARG R 256 " --> pdb=" O GLU R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 262 Processing helix chain 'R' and resid 264 through 266 No H-bonds generated for 'chain 'R' and resid 264 through 266' Processing helix chain 'R' and resid 274 through 284 Processing helix chain 'R' and resid 287 through 295 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 309 through 320 Processing helix chain 'R' and resid 335 through 348 removed outlier: 4.972A pdb=" N VAL R 339 " --> pdb=" O LYS R 336 " (cutoff:3.500A) Processing helix chain 'R' and resid 351 through 354 removed outlier: 3.856A pdb=" N GLN R 354 " --> pdb=" O THR R 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 351 through 354' Processing helix chain 'R' and resid 359 through 365 Processing helix chain 'R' and resid 367 through 372 removed outlier: 3.511A pdb=" N VAL R 370 " --> pdb=" O PRO R 367 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 60 Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'S' and resid 79 through 91 Processing helix chain 'S' and resid 113 through 125 Processing helix chain 'S' and resid 137 through 145 Processing helix chain 'S' and resid 172 through 174 No H-bonds generated for 'chain 'S' and resid 172 through 174' Processing helix chain 'S' and resid 182 through 196 Processing helix chain 'S' and resid 203 through 215 Processing helix chain 'S' and resid 223 through 231 Processing helix chain 'S' and resid 252 through 256 removed outlier: 3.508A pdb=" N ARG S 256 " --> pdb=" O GLU S 253 " (cutoff:3.500A) Processing helix chain 'S' and resid 258 through 262 Processing helix chain 'S' and resid 264 through 266 No H-bonds generated for 'chain 'S' and resid 264 through 266' Processing helix chain 'S' and resid 274 through 284 Processing helix chain 'S' and resid 287 through 295 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 309 through 320 Processing helix chain 'S' and resid 335 through 348 removed outlier: 4.972A pdb=" N VAL S 339 " --> pdb=" O LYS S 336 " (cutoff:3.500A) Processing helix chain 'S' and resid 351 through 354 removed outlier: 3.855A pdb=" N GLN S 354 " --> pdb=" O THR S 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 351 through 354' Processing helix chain 'S' and resid 359 through 365 Processing helix chain 'S' and resid 367 through 372 removed outlier: 3.510A pdb=" N VAL S 370 " --> pdb=" O PRO S 367 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 60 Processing helix chain 'T' and resid 62 through 64 No H-bonds generated for 'chain 'T' and resid 62 through 64' Processing helix chain 'T' and resid 79 through 91 Processing helix chain 'T' and resid 113 through 125 Processing helix chain 'T' and resid 137 through 145 Processing helix chain 'T' and resid 172 through 174 No H-bonds generated for 'chain 'T' and resid 172 through 174' Processing helix chain 'T' and resid 182 through 196 Processing helix chain 'T' and resid 203 through 215 Processing helix chain 'T' and resid 223 through 231 Processing helix chain 'T' and resid 252 through 256 removed outlier: 3.508A pdb=" N ARG T 256 " --> pdb=" O GLU T 253 " (cutoff:3.500A) Processing helix chain 'T' and resid 258 through 262 Processing helix chain 'T' and resid 264 through 266 No H-bonds generated for 'chain 'T' and resid 264 through 266' Processing helix chain 'T' and resid 274 through 284 Processing helix chain 'T' and resid 287 through 295 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 309 through 320 Processing helix chain 'T' and resid 335 through 348 removed outlier: 4.972A pdb=" N VAL T 339 " --> pdb=" O LYS T 336 " (cutoff:3.500A) Processing helix chain 'T' and resid 351 through 354 removed outlier: 3.855A pdb=" N GLN T 354 " --> pdb=" O THR T 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 351 through 354' Processing helix chain 'T' and resid 359 through 365 Processing helix chain 'T' and resid 367 through 372 removed outlier: 3.510A pdb=" N VAL T 370 " --> pdb=" O PRO T 367 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 60 Processing helix chain 'U' and resid 62 through 64 No H-bonds generated for 'chain 'U' and resid 62 through 64' Processing helix chain 'U' and resid 79 through 91 Processing helix chain 'U' and resid 113 through 125 Processing helix chain 'U' and resid 137 through 145 Processing helix chain 'U' and resid 172 through 174 No H-bonds generated for 'chain 'U' and resid 172 through 174' Processing helix chain 'U' and resid 182 through 196 Processing helix chain 'U' and resid 203 through 215 Processing helix chain 'U' and resid 223 through 231 Processing helix chain 'U' and resid 252 through 256 removed outlier: 3.508A pdb=" N ARG U 256 " --> pdb=" O GLU U 253 " (cutoff:3.500A) Processing helix chain 'U' and resid 258 through 262 Processing helix chain 'U' and resid 264 through 266 No H-bonds generated for 'chain 'U' and resid 264 through 266' Processing helix chain 'U' and resid 274 through 284 Processing helix chain 'U' and resid 287 through 295 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 309 through 320 Processing helix chain 'U' and resid 335 through 348 removed outlier: 4.972A pdb=" N VAL U 339 " --> pdb=" O LYS U 336 " (cutoff:3.500A) Processing helix chain 'U' and resid 351 through 354 removed outlier: 3.856A pdb=" N GLN U 354 " --> pdb=" O THR U 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 351 through 354' Processing helix chain 'U' and resid 359 through 365 Processing helix chain 'U' and resid 367 through 372 removed outlier: 3.511A pdb=" N VAL U 370 " --> pdb=" O PRO U 367 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 8 through 11 removed outlier: 3.659A pdb=" N GLY A 20 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 11 " --> pdb=" O LYS A 18 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 109 through 113 removed outlier: 6.646A pdb=" N GLY A 138 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU A 112 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR A 140 " --> pdb=" O LEU A 112 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 165 through 169 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= D, 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= E, first strand: chain 'B' and resid 106 through 108 removed outlier: 4.015A pdb=" N LYS B 19 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS B 20 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS B 30 " --> pdb=" O CYS B 20 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 55 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= G, first strand: chain 'B' and resid 242 through 245 removed outlier: 4.284A pdb=" N TYR B 244 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE B 252 " --> pdb=" O TYR B 244 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 300 through 302 removed outlier: 6.491A pdb=" N ARG B 343 " --> pdb=" O ILE B 301 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, 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) removed outlier: 3.726A pdb=" N CYS C 346 " --> pdb=" O SER C 333 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 14 through 16 removed outlier: 4.065A pdb=" N ILE C 34 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS C 46 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLU C 36 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN C 44 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N SER C 38 " --> pdb=" O TRP C 42 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TRP C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 58 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) Processing sheet with id= L, first strand: chain 'C' and resid 80 through 82 removed outlier: 3.801A pdb=" N THR C 85 " --> pdb=" O LYS C 82 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 132 through 137 removed outlier: 3.885A pdb=" N VAL C 133 " --> pdb=" O TYR C 124 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR C 124 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N CYS C 101 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 166 through 170 removed outlier: 4.497A pdb=" N ARG C 167 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 157 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER C 147 " --> pdb=" O GLY C 160 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 216 through 221 removed outlier: 4.154A pdb=" N THR C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 257 through 260 removed outlier: 4.140A pdb=" N THR C 271 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing sheet with id= Q, 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) Processing sheet with id= R, first strand: chain 'D' and resid 54 through 58 removed outlier: 3.653A pdb=" N VAL D 55 " --> pdb=" O TYR D 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 152 through 157 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= T, first strand: chain 'F' and resid 60 through 63 removed outlier: 3.642A pdb=" N VAL F 72 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 132 through 136 removed outlier: 7.173A pdb=" N THR H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ALA H 135 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE H 31 " --> pdb=" O VAL H 17 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 151 through 154 Processing sheet with id= W, first strand: chain 'H' and resid 160 through 163 removed outlier: 3.509A pdb=" N MET H 176 " --> pdb=" O ASN H 162 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 238 through 241 Processing sheet with id= Y, first strand: chain 'I' and resid 132 through 136 removed outlier: 7.172A pdb=" N THR I 103 " --> pdb=" O TYR I 133 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ALA I 135 " --> pdb=" O THR I 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU I 105 " --> pdb=" O ALA I 135 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU I 8 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N THR I 106 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE I 31 " --> pdb=" O VAL I 17 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 35 through 37 Processing sheet with id= AA, first strand: chain 'I' and resid 151 through 154 Processing sheet with id= AB, first strand: chain 'I' and resid 160 through 163 removed outlier: 3.510A pdb=" N MET I 176 " --> pdb=" O ASN I 162 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 238 through 241 Processing sheet with id= AD, first strand: chain 'J' and resid 132 through 136 removed outlier: 7.172A pdb=" N THR J 103 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ALA J 135 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU J 105 " --> pdb=" O ALA J 135 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU J 8 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR J 106 " --> pdb=" O LEU J 8 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE J 31 " --> pdb=" O VAL J 17 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 35 through 37 Processing sheet with id= AF, first strand: chain 'J' and resid 151 through 154 Processing sheet with id= AG, first strand: chain 'J' and resid 160 through 163 removed outlier: 3.510A pdb=" N MET J 176 " --> pdb=" O ASN J 162 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 238 through 241 Processing sheet with id= AI, first strand: chain 'K' and resid 132 through 136 removed outlier: 7.173A pdb=" N THR K 103 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ALA K 135 " --> pdb=" O THR K 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU K 105 " --> pdb=" O ALA K 135 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE K 31 " --> pdb=" O VAL K 17 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'K' and resid 35 through 37 Processing sheet with id= AK, first strand: chain 'K' and resid 151 through 154 Processing sheet with id= AL, first strand: chain 'K' and resid 160 through 163 removed outlier: 3.509A pdb=" N MET K 176 " --> pdb=" O ASN K 162 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'K' and resid 238 through 241 Processing sheet with id= AN, first strand: chain 'L' and resid 132 through 136 removed outlier: 7.173A pdb=" N THR L 103 " --> pdb=" O TYR L 133 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ALA L 135 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU L 105 " --> pdb=" O ALA L 135 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU L 8 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR L 106 " --> pdb=" O LEU L 8 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE L 31 " --> pdb=" O VAL L 17 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'L' and resid 35 through 37 Processing sheet with id= AP, first strand: chain 'L' and resid 151 through 154 Processing sheet with id= AQ, first strand: chain 'L' and resid 160 through 163 removed outlier: 3.511A pdb=" N MET L 176 " --> pdb=" O ASN L 162 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'L' and resid 238 through 241 Processing sheet with id= AS, first strand: chain 'M' and resid 132 through 136 removed outlier: 7.173A pdb=" N THR M 103 " --> pdb=" O TYR M 133 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ALA M 135 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU M 105 " --> pdb=" O ALA M 135 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU M 8 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR M 106 " --> pdb=" O LEU M 8 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS M 10 " --> pdb=" O THR M 106 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE M 31 " --> pdb=" O VAL M 17 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'M' and resid 35 through 37 Processing sheet with id= AU, first strand: chain 'M' and resid 151 through 154 Processing sheet with id= AV, first strand: chain 'M' and resid 160 through 163 removed outlier: 3.510A pdb=" N MET M 176 " --> pdb=" O ASN M 162 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'M' and resid 238 through 241 Processing sheet with id= AX, first strand: chain 'N' and resid 132 through 136 removed outlier: 7.173A pdb=" N THR N 103 " --> pdb=" O TYR N 133 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ALA N 135 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU N 105 " --> pdb=" O ALA N 135 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU N 8 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N THR N 106 " --> pdb=" O LEU N 8 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS N 10 " --> pdb=" O THR N 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE N 31 " --> pdb=" O VAL N 17 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'N' and resid 35 through 37 Processing sheet with id= AZ, first strand: chain 'N' and resid 151 through 154 Processing sheet with id= BA, first strand: chain 'N' and resid 160 through 163 removed outlier: 3.509A pdb=" N MET N 176 " --> pdb=" O ASN N 162 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'N' and resid 238 through 241 Processing sheet with id= BC, first strand: chain 'O' and resid 132 through 136 removed outlier: 7.173A pdb=" N THR O 103 " --> pdb=" O TYR O 133 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ALA O 135 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU O 105 " --> pdb=" O ALA O 135 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU O 8 " --> pdb=" O LEU O 104 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR O 106 " --> pdb=" O LEU O 8 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE O 31 " --> pdb=" O VAL O 17 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'O' and resid 35 through 38 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= BE, first strand: chain 'O' and resid 151 through 154 Processing sheet with id= BF, first strand: chain 'O' and resid 160 through 163 removed outlier: 3.509A pdb=" N MET O 176 " --> pdb=" O ASN O 162 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'O' and resid 238 through 241 Processing sheet with id= BH, first strand: chain 'P' and resid 132 through 136 removed outlier: 7.173A pdb=" N THR P 103 " --> pdb=" O TYR P 133 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ALA P 135 " --> pdb=" O THR P 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU P 105 " --> pdb=" O ALA P 135 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU P 8 " --> pdb=" O LEU P 104 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR P 106 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS P 10 " --> pdb=" O THR P 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE P 31 " --> pdb=" O VAL P 17 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'P' and resid 35 through 37 Processing sheet with id= BJ, first strand: chain 'P' and resid 151 through 154 Processing sheet with id= BK, first strand: chain 'P' and resid 160 through 163 removed outlier: 3.509A pdb=" N MET P 176 " --> pdb=" O ASN P 162 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'P' and resid 238 through 241 Processing sheet with id= BM, first strand: chain 'Q' and resid 132 through 136 removed outlier: 7.172A pdb=" N THR Q 103 " --> pdb=" O TYR Q 133 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ALA Q 135 " --> pdb=" O THR Q 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU Q 105 " --> pdb=" O ALA Q 135 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR Q 106 " --> pdb=" O LEU Q 8 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS Q 10 " --> pdb=" O THR Q 106 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE Q 31 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'Q' and resid 35 through 37 Processing sheet with id= BO, first strand: chain 'Q' and resid 151 through 154 Processing sheet with id= BP, first strand: chain 'Q' and resid 160 through 163 removed outlier: 3.510A pdb=" N MET Q 176 " --> pdb=" O ASN Q 162 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'Q' and resid 238 through 241 Processing sheet with id= BR, first strand: chain 'R' and resid 132 through 136 removed outlier: 7.172A pdb=" N THR R 103 " --> pdb=" O TYR R 133 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ALA R 135 " --> pdb=" O THR R 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU R 105 " --> pdb=" O ALA R 135 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU R 8 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR R 106 " --> pdb=" O LEU R 8 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS R 10 " --> pdb=" O THR R 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE R 31 " --> pdb=" O VAL R 17 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'R' and resid 35 through 37 Processing sheet with id= BT, first strand: chain 'R' and resid 151 through 154 Processing sheet with id= BU, first strand: chain 'R' and resid 160 through 163 removed outlier: 3.510A pdb=" N MET R 176 " --> pdb=" O ASN R 162 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'R' and resid 238 through 241 Processing sheet with id= BW, first strand: chain 'S' and resid 132 through 136 removed outlier: 7.173A pdb=" N THR S 103 " --> pdb=" O TYR S 133 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ALA S 135 " --> pdb=" O THR S 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU S 105 " --> pdb=" O ALA S 135 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU S 8 " --> pdb=" O LEU S 104 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR S 106 " --> pdb=" O LEU S 8 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N CYS S 10 " --> pdb=" O THR S 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE S 31 " --> pdb=" O VAL S 17 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'S' and resid 35 through 37 Processing sheet with id= BY, first strand: chain 'S' and resid 151 through 154 Processing sheet with id= BZ, first strand: chain 'S' and resid 160 through 163 removed outlier: 3.509A pdb=" N MET S 176 " --> pdb=" O ASN S 162 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'S' and resid 238 through 241 Processing sheet with id= CB, first strand: chain 'T' and resid 132 through 136 removed outlier: 7.173A pdb=" N THR T 103 " --> pdb=" O TYR T 133 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ALA T 135 " --> pdb=" O THR T 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU T 105 " --> pdb=" O ALA T 135 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU T 8 " --> pdb=" O LEU T 104 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR T 106 " --> pdb=" O LEU T 8 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N CYS T 10 " --> pdb=" O THR T 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE T 31 " --> pdb=" O VAL T 17 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'T' and resid 35 through 37 Processing sheet with id= CD, first strand: chain 'T' and resid 151 through 154 Processing sheet with id= CE, first strand: chain 'T' and resid 160 through 163 removed outlier: 3.509A pdb=" N MET T 176 " --> pdb=" O ASN T 162 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'T' and resid 238 through 241 Processing sheet with id= CG, first strand: chain 'U' and resid 132 through 136 removed outlier: 7.173A pdb=" N THR U 103 " --> pdb=" O TYR U 133 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ALA U 135 " --> pdb=" O THR U 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU U 105 " --> pdb=" O ALA U 135 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU U 8 " --> pdb=" O LEU U 104 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N THR U 106 " --> pdb=" O LEU U 8 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS U 10 " --> pdb=" O THR U 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE U 31 " --> pdb=" O VAL U 17 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'U' and resid 35 through 37 Processing sheet with id= CI, first strand: chain 'U' and resid 151 through 154 Processing sheet with id= CJ, first strand: chain 'U' and resid 160 through 163 removed outlier: 3.510A pdb=" N MET U 176 " --> pdb=" O ASN U 162 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'U' and resid 238 through 241 1949 hydrogen bonds defined for protein. 4863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.61 Time building geometry restraints manager: 21.15 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: 12962 1.44 - 1.58: 29267 1.58 - 1.71: 98 1.71 - 1.84: 435 Bond restraints: 51631 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 51626 not shown) Histogram of bond angle deviations from ideal: 95.95 - 103.75: 756 103.75 - 111.54: 23857 111.54 - 119.34: 18923 119.34 - 127.14: 26369 127.14 - 134.93: 541 Bond angle restraints: 70446 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 70441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.46: 30219 34.46 - 68.91: 480 68.91 - 103.37: 38 103.37 - 137.83: 21 137.83 - 172.28: 7 Dihedral angle restraints: 30765 sinusoidal: 9963 harmonic: 20802 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 30762 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: 9225 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 9222 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.05: 42 2.05 - 2.76: 8927 2.76 - 3.47: 73753 3.47 - 4.19: 106652 4.19 - 4.90: 192204 Nonbonded interactions: 381578 Sorted by model distance: nonbonded pdb=" N TRP f 1 " pdb=" C ALA f 7 " model vdw 1.331 3.350 nonbonded pdb=" N TRP m 1 " pdb=" C ALA m 7 " model vdw 1.332 3.350 nonbonded pdb=" N TRP j 1 " pdb=" C ALA j 7 " model vdw 1.332 3.350 nonbonded pdb=" N TRP o 1 " pdb=" C ALA o 7 " model vdw 1.332 3.350 nonbonded pdb=" N TRP e 1 " pdb=" C ALA e 7 " model vdw 1.332 3.350 ... (remaining 381573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '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: 0.000 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 12.970 Check model and map are aligned: 0.700 Set scattering table: 0.470 Process input model: 130.890 Find NCS groups from input model: 5.070 Set up NCS constraints: 0.530 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.810 ------------------------------------------------------------------------------- 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 51631 Z= 0.658 Angle : 0.895 13.813 70446 Z= 0.451 Chirality : 0.048 0.458 8177 Planarity : 0.003 0.059 9225 Dihedral : 14.368 172.282 17355 Min Nonbonded Distance : 1.331 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 fitting. rotamer outliers: 19 poor density : 1273 time to evaluate : 5.787 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: 0.6416 time to fit residues: 1357.6249 Evaluate side-chains 1162 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1147 time to evaluate : 5.274 ------------------------------------------------------------------------------- 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: 0.7980 chunk 297 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 chunk 361 optimal weight: 50.0000 chunk 286 optimal weight: 9.9990 chunk 554 optimal weight: 0.0670 chunk 214 optimal weight: 0.6980 chunk 336 optimal weight: 50.0000 chunk 412 optimal weight: 0.7980 chunk 642 optimal weight: 0.3980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN 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 G 129 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 360 GLN ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 87 HIS O 92 ASN O 101 HIS O 121 GLN O 314 GLN ** P 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 173 HIS R 173 HIS S 246 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 51631 Z= 0.195 Angle : 0.633 10.162 70446 Z= 0.308 Chirality : 0.046 0.210 8177 Planarity : 0.004 0.056 9225 Dihedral : 9.689 174.046 8038 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.25 % Allowed : 11.25 % 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: 0.74 (0.10), residues: 7041 helix: 1.45 (0.10), residues: 2678 sheet: 0.81 (0.17), residues: 1018 loop : -0.35 (0.11), residues: 3345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP h 1 HIS 0.014 0.001 HIS P 275 PHE 0.023 0.002 PHE B 32 TYR 0.022 0.001 TYR B 192 ARG 0.010 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 1307 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1213 time to evaluate : 5.092 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: A 64 ASP cc_start: 0.8157 (p0) cc_final: 0.7931 (p0) REVERT: A 89 MET cc_start: 0.7916 (tpp) cc_final: 0.7671 (tpp) REVERT: A 99 LYS cc_start: 0.7420 (mtpp) cc_final: 0.6846 (mtmm) REVERT: A 114 GLU cc_start: 0.7498 (pm20) cc_final: 0.7286 (pm20) REVERT: A 135 ASN cc_start: 0.7859 (m110) cc_final: 0.7533 (m-40) REVERT: A 233 TYR cc_start: 0.5603 (p90) cc_final: 0.4835 (p90) REVERT: A 305 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7493 (mm-40) REVERT: A 326 THR cc_start: 0.7752 (p) cc_final: 0.7502 (p) REVERT: A 402 GLU cc_start: 0.6938 (pm20) cc_final: 0.6478 (pm20) REVERT: B 85 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.7131 (ttm) REVERT: B 86 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7872 (ttpp) REVERT: B 145 THR cc_start: 0.6645 (p) cc_final: 0.6443 (p) REVERT: B 146 LEU cc_start: 0.7380 (mp) cc_final: 0.7045 (mp) REVERT: B 158 ASP cc_start: 0.7146 (t0) cc_final: 0.6856 (t0) REVERT: B 226 ASN cc_start: 0.8262 (t0) cc_final: 0.7812 (t0) REVERT: B 263 GLU cc_start: 0.6610 (mm-30) cc_final: 0.6253 (tp30) REVERT: B 280 GLU cc_start: 0.5497 (tm-30) cc_final: 0.5253 (tm-30) REVERT: B 296 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7332 (tp30) REVERT: B 318 GLU cc_start: 0.7533 (pp20) cc_final: 0.7248 (tm-30) REVERT: B 371 PHE cc_start: 0.6066 (t80) cc_final: 0.5750 (t80) REVERT: C 13 CYS cc_start: 0.6748 (t) cc_final: 0.6321 (t) REVERT: C 41 LYS cc_start: 0.7631 (mmmm) cc_final: 0.7300 (mmmm) REVERT: C 42 TRP cc_start: 0.7967 (m100) cc_final: 0.7193 (m100) REVERT: C 56 THR cc_start: 0.7871 (p) cc_final: 0.7502 (m) REVERT: C 95 ILE cc_start: 0.8034 (mm) cc_final: 0.7773 (mm) REVERT: C 104 TRP cc_start: 0.7344 (m100) cc_final: 0.6771 (m100) REVERT: C 148 LEU cc_start: 0.8090 (mp) cc_final: 0.7851 (mt) REVERT: C 300 GLU cc_start: 0.5482 (tm-30) cc_final: 0.5155 (tm-30) REVERT: C 335 LEU cc_start: 0.6834 (mm) cc_final: 0.6626 (mm) REVERT: C 358 ASP cc_start: 0.7913 (m-30) cc_final: 0.7696 (m-30) REVERT: D 184 GLU cc_start: 0.6972 (mp0) cc_final: 0.6640 (mp0) REVERT: D 247 PHE cc_start: 0.6509 (t80) cc_final: 0.6251 (t80) REVERT: E 14 LYS cc_start: 0.8224 (mmmt) cc_final: 0.7961 (mmmt) REVERT: E 68 LEU cc_start: 0.6784 (mm) cc_final: 0.6582 (mt) REVERT: E 95 MET cc_start: 0.7594 (mtm) cc_final: 0.7372 (mtm) REVERT: E 155 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8625 (mmtm) REVERT: F 91 MET cc_start: 0.7590 (mmt) cc_final: 0.7204 (mmm) REVERT: F 95 MET cc_start: 0.5279 (mmp) cc_final: 0.4745 (mmp) REVERT: F 115 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8336 (m) REVERT: F 163 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6511 (tm-30) REVERT: G 86 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7292 (t80) REVERT: H 12 ASN cc_start: 0.6816 (p0) cc_final: 0.6546 (p0) REVERT: H 16 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7157 (mp) REVERT: H 18 LYS cc_start: 0.7621 (mppt) cc_final: 0.7047 (mmmm) REVERT: H 50 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8035 (mtmt) REVERT: H 119 MET cc_start: 0.4717 (ptt) cc_final: 0.3967 (ptt) REVERT: H 123 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7170 (mpp) REVERT: H 262 PHE cc_start: 0.7936 (m-10) cc_final: 0.7733 (m-10) REVERT: H 276 GLU cc_start: 0.7011 (tp30) cc_final: 0.6190 (tm-30) REVERT: I 16 LEU cc_start: 0.6588 (tt) cc_final: 0.5982 (mt) REVERT: I 72 GLU cc_start: 0.6920 (tt0) cc_final: 0.6613 (pt0) REVERT: I 100 GLU cc_start: 0.7653 (tp30) cc_final: 0.7179 (tp30) REVERT: I 107 GLU cc_start: 0.6493 (pm20) cc_final: 0.5871 (pm20) REVERT: I 238 LYS cc_start: 0.6662 (mttp) cc_final: 0.6446 (mttp) REVERT: I 259 GLU cc_start: 0.6822 (tp30) cc_final: 0.6156 (tp30) REVERT: I 314 GLN cc_start: 0.6783 (tp-100) cc_final: 0.6440 (tp-100) REVERT: N 89 THR cc_start: 0.5316 (m) cc_final: 0.4459 (p) REVERT: N 154 ASP cc_start: 0.7387 (t0) cc_final: 0.6722 (t0) REVERT: N 176 MET cc_start: 0.6894 (mtp) cc_final: 0.6479 (mtt) REVERT: N 191 LYS cc_start: 0.7402 (tptt) cc_final: 0.7137 (tppt) REVERT: N 244 ASP cc_start: 0.7445 (p0) cc_final: 0.7199 (p0) REVERT: N 282 ILE cc_start: 0.7259 (tt) cc_final: 0.6968 (pt) REVERT: N 357 ILE cc_start: 0.7809 (mm) cc_final: 0.7571 (tp) REVERT: O 62 ARG cc_start: 0.7548 (ptt-90) cc_final: 0.7044 (ptt-90) REVERT: O 132 MET cc_start: 0.7968 (ppp) cc_final: 0.7704 (ppp) REVERT: O 190 MET cc_start: 0.6879 (ttm) cc_final: 0.6516 (ttp) REVERT: O 195 GLU cc_start: 0.7404 (pt0) cc_final: 0.7163 (pt0) REVERT: O 283 MET cc_start: 0.7185 (mmp) cc_final: 0.6947 (mmp) REVERT: O 328 LYS cc_start: 0.7279 (tptt) cc_final: 0.7047 (tptt) REVERT: P 91 TYR cc_start: 0.7930 (m-80) cc_final: 0.7692 (m-80) REVERT: P 111 ASN cc_start: 0.7115 (m-40) cc_final: 0.6775 (m-40) REVERT: P 211 ASP cc_start: 0.7372 (t70) cc_final: 0.7166 (t70) REVERT: P 214 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6785 (mt-10) REVERT: P 226 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6822 (mm-30) REVERT: Q 68 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7893 (mtpp) REVERT: Q 72 GLU cc_start: 0.5900 (tm-30) cc_final: 0.5677 (tm-30) REVERT: Q 107 GLU cc_start: 0.7197 (pt0) cc_final: 0.6915 (pt0) REVERT: Q 116 ARG cc_start: 0.7538 (ttm170) cc_final: 0.6932 (mmm-85) REVERT: Q 171 LEU cc_start: 0.8010 (mm) cc_final: 0.7775 (mp) REVERT: Q 190 MET cc_start: 0.6518 (mtt) cc_final: 0.6302 (mtp) REVERT: Q 210 ARG cc_start: 0.7443 (ttm-80) cc_final: 0.7206 (ttm170) REVERT: Q 214 GLU cc_start: 0.6695 (mt-10) cc_final: 0.6276 (tt0) REVERT: Q 255 PHE cc_start: 0.6351 (p90) cc_final: 0.6131 (p90) REVERT: Q 325 MET cc_start: 0.7753 (pmm) cc_final: 0.6042 (ptt) REVERT: R 47 MET cc_start: 0.4186 (mpp) cc_final: 0.3944 (mmm) REVERT: R 82 MET cc_start: 0.7160 (mmm) cc_final: 0.6730 (tpp) REVERT: R 121 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7396 (tm-30) REVERT: R 151 ILE cc_start: 0.7914 (tp) cc_final: 0.7516 (pt) REVERT: R 176 MET cc_start: 0.7419 (mtt) cc_final: 0.7149 (mtp) REVERT: R 248 ILE cc_start: 0.8547 (mm) cc_final: 0.8021 (tt) REVERT: R 296 ASN cc_start: 0.7455 (m-40) cc_final: 0.7213 (m-40) REVERT: R 334 GLU cc_start: 0.7510 (pm20) cc_final: 0.7098 (pm20) REVERT: R 364 GLU cc_start: 0.8118 (pp20) cc_final: 0.7916 (pp20) REVERT: S 66 THR cc_start: 0.7350 (m) cc_final: 0.7112 (p) REVERT: S 120 THR cc_start: 0.7441 (m) cc_final: 0.7049 (t) REVERT: S 176 MET cc_start: 0.6495 (mmm) cc_final: 0.6112 (mmm) REVERT: S 213 LYS cc_start: 0.7547 (ttpt) cc_final: 0.7327 (ttpt) REVERT: S 222 ASP cc_start: 0.6695 (t70) cc_final: 0.6318 (t70) REVERT: S 283 MET cc_start: 0.6864 (mmm) cc_final: 0.6433 (mmm) REVERT: S 325 MET cc_start: 0.5905 (pmm) cc_final: 0.5692 (pmm) REVERT: S 334 GLU cc_start: 0.5874 (pm20) cc_final: 0.5638 (pm20) REVERT: i 5 CYS cc_start: 0.5420 (OUTLIER) cc_final: 0.5140 (m) REVERT: n 5 CYS cc_start: 0.0819 (OUTLIER) cc_final: 0.0032 (p) outliers start: 94 outliers final: 48 residues processed: 1238 average time/residue: 0.6659 time to fit residues: 1370.3442 Evaluate side-chains 1224 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1169 time to evaluate : 5.041 ------------------------------------------------------------------------------- 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 71 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 259 PHE 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 G residue 86 PHE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 159 VAL 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 30 VAL Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 311 ASP 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 O residue 314 GLN Chi-restraints excluded: chain P residue 80 ASP 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 305 MET 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 232 SER 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 b residue 5 CYS Chi-restraints excluded: chain d residue 5 CYS Chi-restraints excluded: chain e residue 5 CYS Chi-restraints excluded: chain i residue 5 CYS Chi-restraints excluded: chain j residue 5 CYS Chi-restraints excluded: chain n residue 5 CYS Chi-restraints excluded: chain o residue 5 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 356 optimal weight: 30.0000 chunk 199 optimal weight: 0.7980 chunk 534 optimal weight: 0.3980 chunk 437 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 643 optimal weight: 0.7980 chunk 694 optimal weight: 0.9990 chunk 572 optimal weight: 0.1980 chunk 637 optimal weight: 0.0470 chunk 219 optimal weight: 0.9990 chunk 515 optimal weight: 0.5980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN B 272 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 ASN ** H 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 87 HIS ** P 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN P 252 ASN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 296 ASN ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 173 HIS R 111 ASN R 173 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 51631 Z= 0.164 Angle : 0.592 9.721 70446 Z= 0.287 Chirality : 0.045 0.216 8177 Planarity : 0.003 0.041 9225 Dihedral : 8.997 170.909 8029 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.84 % Allowed : 14.26 % Favored : 82.90 % 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: 0.54 (0.10), residues: 7041 helix: 1.19 (0.10), residues: 2688 sheet: 0.60 (0.17), residues: 1011 loop : -0.34 (0.11), residues: 3342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 79 HIS 0.011 0.001 HIS R 173 PHE 0.024 0.001 PHE B 32 TYR 0.025 0.001 TYR D 43 ARG 0.007 0.000 ARG S 290 *********************** 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 1305 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1186 time to evaluate : 5.371 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 64 ASP cc_start: 0.8172 (p0) cc_final: 0.7956 (p0) REVERT: A 97 ILE cc_start: 0.8580 (tt) cc_final: 0.8333 (tp) REVERT: A 114 GLU cc_start: 0.7459 (pm20) cc_final: 0.7238 (pm20) REVERT: A 130 MET cc_start: 0.7201 (mmm) cc_final: 0.6882 (tpp) REVERT: A 135 ASN cc_start: 0.7884 (m110) cc_final: 0.7645 (m-40) REVERT: A 233 TYR cc_start: 0.5540 (p90) cc_final: 0.4363 (p90) REVERT: A 326 THR cc_start: 0.7758 (p) cc_final: 0.7507 (p) REVERT: A 371 HIS cc_start: 0.6760 (p-80) cc_final: 0.6415 (p-80) REVERT: B 86 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7884 (ttpp) REVERT: B 106 LYS cc_start: 0.8283 (mmtm) cc_final: 0.7944 (mmmt) REVERT: B 136 VAL cc_start: 0.7238 (m) cc_final: 0.6863 (p) REVERT: B 145 THR cc_start: 0.6637 (p) cc_final: 0.6367 (p) REVERT: B 146 LEU cc_start: 0.7387 (mp) cc_final: 0.6690 (mt) REVERT: B 158 ASP cc_start: 0.7147 (t0) cc_final: 0.6891 (t0) REVERT: B 225 TYR cc_start: 0.7072 (t80) cc_final: 0.6787 (t80) REVERT: B 263 GLU cc_start: 0.6611 (mm-30) cc_final: 0.6076 (mm-30) REVERT: B 280 GLU cc_start: 0.5461 (tm-30) cc_final: 0.5241 (tm-30) REVERT: B 296 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7301 (tp30) REVERT: B 318 GLU cc_start: 0.7571 (pp20) cc_final: 0.7362 (pp20) REVERT: C 13 CYS cc_start: 0.6581 (t) cc_final: 0.6360 (t) REVERT: C 41 LYS cc_start: 0.7512 (mmmm) cc_final: 0.7135 (mmmm) REVERT: C 42 TRP cc_start: 0.7961 (m100) cc_final: 0.7366 (m100) REVERT: C 56 THR cc_start: 0.7909 (p) cc_final: 0.7540 (m) REVERT: C 95 ILE cc_start: 0.7992 (mm) cc_final: 0.7736 (mm) REVERT: C 104 TRP cc_start: 0.7381 (m100) cc_final: 0.6268 (m100) REVERT: C 108 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6553 (mm-30) REVERT: C 110 LYS cc_start: 0.8502 (ptpt) cc_final: 0.8204 (pttt) REVERT: C 209 CYS cc_start: 0.7642 (t) cc_final: 0.7288 (t) REVERT: C 300 GLU cc_start: 0.5550 (tm-30) cc_final: 0.5189 (tm-30) REVERT: C 335 LEU cc_start: 0.7201 (mm) cc_final: 0.6951 (mm) REVERT: D 33 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8004 (t) REVERT: D 119 ASN cc_start: 0.7066 (t0) cc_final: 0.6753 (t0) REVERT: D 158 LYS cc_start: 0.7307 (tppt) cc_final: 0.7075 (mmmt) REVERT: E 14 LYS cc_start: 0.8205 (mmmt) cc_final: 0.7937 (mmmt) REVERT: E 68 LEU cc_start: 0.6721 (mm) cc_final: 0.6513 (mt) REVERT: E 93 LYS cc_start: 0.8354 (mmmt) cc_final: 0.8060 (mptp) REVERT: E 95 MET cc_start: 0.7708 (mtm) cc_final: 0.7464 (mtm) REVERT: E 155 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8602 (mmtm) REVERT: F 115 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8394 (m) REVERT: F 163 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6516 (tm-30) REVERT: G 86 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7342 (t80) REVERT: H 12 ASN cc_start: 0.6947 (p0) cc_final: 0.6571 (p0) REVERT: H 18 LYS cc_start: 0.7634 (mppt) cc_final: 0.7233 (mmmm) REVERT: H 71 ILE cc_start: 0.5843 (OUTLIER) cc_final: 0.5641 (pt) REVERT: H 83 GLU cc_start: 0.6817 (pp20) cc_final: 0.6509 (pp20) REVERT: H 256 ARG cc_start: 0.7098 (ttm170) cc_final: 0.6747 (ttp-170) REVERT: H 276 GLU cc_start: 0.7062 (tp30) cc_final: 0.6246 (tm-30) REVERT: I 72 GLU cc_start: 0.6748 (tt0) cc_final: 0.6364 (tt0) REVERT: I 100 GLU cc_start: 0.7724 (tp30) cc_final: 0.7260 (tp30) REVERT: I 107 GLU cc_start: 0.6592 (pm20) cc_final: 0.6091 (pm20) REVERT: I 119 MET cc_start: 0.6687 (mtm) cc_final: 0.6293 (mtm) REVERT: I 121 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7753 (tm-30) REVERT: I 198 TYR cc_start: 0.7248 (m-80) cc_final: 0.6927 (m-10) REVERT: I 238 LYS cc_start: 0.6549 (mttp) cc_final: 0.6218 (mtmm) REVERT: I 259 GLU cc_start: 0.6819 (tp30) cc_final: 0.6178 (tp30) REVERT: N 71 ILE cc_start: 0.7210 (tt) cc_final: 0.6373 (pt) REVERT: N 72 GLU cc_start: 0.6950 (tp30) cc_final: 0.6383 (mp0) REVERT: N 154 ASP cc_start: 0.7413 (t0) cc_final: 0.6735 (t0) REVERT: N 176 MET cc_start: 0.6775 (mtp) cc_final: 0.6510 (mtt) REVERT: N 191 LYS cc_start: 0.7477 (tptt) cc_final: 0.7138 (tppt) REVERT: N 238 LYS cc_start: 0.7463 (mmtm) cc_final: 0.6991 (mmtm) REVERT: O 62 ARG cc_start: 0.7564 (ptt-90) cc_final: 0.7015 (ptt-90) REVERT: O 153 LEU cc_start: 0.7879 (tp) cc_final: 0.7642 (tt) REVERT: O 190 MET cc_start: 0.6914 (ttm) cc_final: 0.6650 (ttp) REVERT: O 227 MET cc_start: 0.7677 (mmm) cc_final: 0.6987 (mmm) REVERT: O 255 PHE cc_start: 0.7531 (p90) cc_final: 0.6966 (p90) REVERT: P 111 ASN cc_start: 0.7281 (m-40) cc_final: 0.6833 (m-40) REVERT: P 123 MET cc_start: 0.7226 (mmm) cc_final: 0.6900 (mmm) REVERT: P 176 MET cc_start: 0.7084 (mtt) cc_final: 0.6598 (mmm) REVERT: P 195 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6291 (pt0) REVERT: P 214 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6635 (mt-10) REVERT: P 226 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6722 (mm-30) REVERT: P 240 TYR cc_start: 0.7813 (t80) cc_final: 0.7558 (t80) REVERT: P 241 GLU cc_start: 0.6504 (tt0) cc_final: 0.6237 (tt0) REVERT: Q 68 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7918 (mtpp) REVERT: Q 107 GLU cc_start: 0.7343 (pt0) cc_final: 0.7038 (pt0) REVERT: Q 116 ARG cc_start: 0.7571 (ttm170) cc_final: 0.7025 (mtt180) REVERT: Q 132 MET cc_start: 0.6478 (OUTLIER) cc_final: 0.6253 (tmm) REVERT: Q 171 LEU cc_start: 0.8026 (mm) cc_final: 0.7702 (mp) REVERT: Q 190 MET cc_start: 0.6651 (mtt) cc_final: 0.6412 (mtp) REVERT: Q 247 VAL cc_start: 0.8150 (t) cc_final: 0.7931 (m) REVERT: Q 255 PHE cc_start: 0.6329 (p90) cc_final: 0.6126 (p90) REVERT: Q 325 MET cc_start: 0.7852 (pmm) cc_final: 0.5896 (ptt) REVERT: Q 360 GLN cc_start: 0.6876 (tp40) cc_final: 0.6619 (tp40) REVERT: R 39 ARG cc_start: 0.6719 (ttp-110) cc_final: 0.6473 (ttp-170) REVERT: R 82 MET cc_start: 0.7261 (mmm) cc_final: 0.7048 (tpt) REVERT: R 121 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7558 (tm-30) REVERT: R 210 ARG cc_start: 0.7642 (tmm-80) cc_final: 0.6886 (ttp80) REVERT: R 248 ILE cc_start: 0.8495 (mm) cc_final: 0.7918 (tt) REVERT: S 66 THR cc_start: 0.7340 (m) cc_final: 0.7077 (p) REVERT: S 120 THR cc_start: 0.7418 (m) cc_final: 0.7073 (t) REVERT: S 195 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6305 (pt0) REVERT: S 213 LYS cc_start: 0.7531 (ttpt) cc_final: 0.7313 (ttpt) REVERT: S 283 MET cc_start: 0.6824 (mmm) cc_final: 0.6343 (mmm) REVERT: S 325 MET cc_start: 0.6108 (pmm) cc_final: 0.5806 (pmm) REVERT: n 5 CYS cc_start: 0.0859 (OUTLIER) cc_final: -0.0105 (p) outliers start: 119 outliers final: 68 residues processed: 1226 average time/residue: 0.6432 time to fit residues: 1299.9480 Evaluate side-chains 1226 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1150 time to evaluate : 5.491 ------------------------------------------------------------------------------- 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 30 ILE Chi-restraints excluded: chain A residue 71 THR 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 26 ASN 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 152 LEU Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 33 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 115 SER Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 159 VAL 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 H residue 360 GLN 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 I residue 311 ASP Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 303 THR 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 304 THR Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 80 ASP Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 195 GLU 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 132 MET Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 191 LYS Chi-restraints excluded: chain R residue 12 ASN Chi-restraints excluded: chain R residue 61 LYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 351 THR Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain d residue 5 CYS Chi-restraints excluded: chain n residue 5 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 635 optimal weight: 9.9990 chunk 483 optimal weight: 1.9990 chunk 333 optimal weight: 30.0000 chunk 71 optimal weight: 3.9990 chunk 306 optimal weight: 10.0000 chunk 431 optimal weight: 0.6980 chunk 645 optimal weight: 20.0000 chunk 683 optimal weight: 40.0000 chunk 337 optimal weight: 20.0000 chunk 611 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 HIS ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 263 GLN H 296 ASN H 360 GLN N 88 HIS N 115 ASN N 137 GLN ** P 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN P 137 GLN P 161 HIS ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 371 HIS S 296 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.197 51631 Z= 0.519 Angle : 0.884 15.022 70446 Z= 0.457 Chirality : 0.056 0.316 8177 Planarity : 0.006 0.086 9225 Dihedral : 9.847 139.206 8025 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.62 % Favored : 93.31 % Rotamer: Outliers : 5.21 % Allowed : 15.79 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.68 (0.10), residues: 7041 helix: 0.14 (0.10), residues: 2601 sheet: 0.12 (0.17), residues: 911 loop : -1.02 (0.11), residues: 3529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.004 TRP n 1 HIS 0.015 0.003 HIS S 161 PHE 0.057 0.003 PHE C 252 TYR 0.037 0.003 TYR F 8 ARG 0.011 0.001 ARG N 312 *********************** 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 1534 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1316 time to evaluate : 5.305 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: A 17 THR cc_start: 0.8397 (m) cc_final: 0.8044 (t) REVERT: A 26 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6645 (mm-30) REVERT: A 94 GLU cc_start: 0.7876 (pp20) cc_final: 0.7598 (pp20) REVERT: A 97 ILE cc_start: 0.8700 (tt) cc_final: 0.8337 (tp) REVERT: A 99 LYS cc_start: 0.7911 (mtpp) cc_final: 0.7402 (mtmm) REVERT: A 104 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7751 (mp0) REVERT: A 130 MET cc_start: 0.8080 (mmm) cc_final: 0.7327 (mpp) REVERT: A 135 ASN cc_start: 0.7715 (m110) cc_final: 0.7361 (m-40) REVERT: A 168 ILE cc_start: 0.7364 (mp) cc_final: 0.7137 (pt) REVERT: A 206 GLN cc_start: 0.7973 (tp40) cc_final: 0.7545 (tm-30) REVERT: A 241 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6528 (mt-10) REVERT: A 296 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.7105 (mt) REVERT: A 371 HIS cc_start: 0.7082 (p-80) cc_final: 0.6416 (p90) REVERT: A 406 SER cc_start: 0.8015 (p) cc_final: 0.7751 (m) REVERT: B 42 ARG cc_start: 0.7705 (mtt90) cc_final: 0.7437 (mtt90) REVERT: B 57 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7934 (p) REVERT: B 86 LYS cc_start: 0.8386 (ttpp) cc_final: 0.8050 (ttpp) REVERT: B 158 ASP cc_start: 0.7361 (t0) cc_final: 0.7146 (t0) REVERT: B 226 ASN cc_start: 0.8480 (t0) cc_final: 0.7969 (t0) REVERT: B 263 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6510 (tp30) REVERT: B 272 ASN cc_start: 0.7859 (p0) cc_final: 0.7513 (p0) REVERT: B 296 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7356 (tp30) REVERT: B 309 MET cc_start: 0.7797 (tpp) cc_final: 0.7408 (tpt) REVERT: B 320 GLU cc_start: 0.6925 (tp30) cc_final: 0.6384 (tp30) REVERT: C 13 CYS cc_start: 0.6994 (t) cc_final: 0.6662 (t) REVERT: C 31 GLU cc_start: 0.7236 (pt0) cc_final: 0.6971 (pt0) REVERT: C 42 TRP cc_start: 0.8193 (m100) cc_final: 0.7875 (m100) REVERT: C 56 THR cc_start: 0.8236 (p) cc_final: 0.8033 (m) REVERT: C 104 TRP cc_start: 0.7538 (m100) cc_final: 0.6700 (m100) REVERT: C 209 CYS cc_start: 0.7747 (t) cc_final: 0.7014 (t) REVERT: C 335 LEU cc_start: 0.7342 (mm) cc_final: 0.6798 (mm) REVERT: C 336 SER cc_start: 0.7366 (m) cc_final: 0.7042 (p) REVERT: C 351 ASP cc_start: 0.8192 (p0) cc_final: 0.7949 (p0) REVERT: D 2 ILE cc_start: 0.8129 (tp) cc_final: 0.7920 (tt) REVERT: D 5 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6635 (tm-30) REVERT: D 42 LEU cc_start: 0.7672 (mm) cc_final: 0.7459 (tp) REVERT: D 158 LYS cc_start: 0.7175 (tppt) cc_final: 0.6906 (mmmt) REVERT: D 241 ILE cc_start: 0.8102 (mt) cc_final: 0.7773 (tt) REVERT: D 247 PHE cc_start: 0.6846 (t80) cc_final: 0.6325 (t80) REVERT: D 259 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8541 (mttt) REVERT: D 265 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7952 (ttm110) REVERT: E 14 LYS cc_start: 0.8367 (mmmt) cc_final: 0.8153 (mmmt) REVERT: E 93 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8166 (mttm) REVERT: E 95 MET cc_start: 0.8014 (mtm) cc_final: 0.7773 (mtm) REVERT: E 155 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8678 (mmtm) REVERT: F 83 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7287 (mt-10) REVERT: F 91 MET cc_start: 0.8333 (mmm) cc_final: 0.7515 (mmt) REVERT: F 93 PHE cc_start: 0.7439 (m-10) cc_final: 0.7199 (m-10) REVERT: F 95 MET cc_start: 0.5822 (mmp) cc_final: 0.5352 (mmp) REVERT: G 86 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.6682 (t80) REVERT: G 90 ASP cc_start: 0.7965 (t70) cc_final: 0.7239 (t70) REVERT: G 108 LYS cc_start: 0.8268 (mttp) cc_final: 0.7735 (tttp) REVERT: H 12 ASN cc_start: 0.7043 (p0) cc_final: 0.6701 (p0) REVERT: H 61 LYS cc_start: 0.8380 (mtmm) cc_final: 0.8094 (mtmm) REVERT: H 65 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5611 (mt) REVERT: H 80 ASP cc_start: 0.7710 (m-30) cc_final: 0.7450 (m-30) REVERT: H 83 GLU cc_start: 0.7203 (pp20) cc_final: 0.6830 (pp20) REVERT: H 84 LYS cc_start: 0.8222 (mttm) cc_final: 0.7363 (mttm) REVERT: H 121 GLN cc_start: 0.8159 (pp30) cc_final: 0.7821 (pp30) REVERT: H 222 ASP cc_start: 0.6943 (t0) cc_final: 0.6623 (t0) REVERT: H 241 GLU cc_start: 0.5731 (tm-30) cc_final: 0.5465 (tm-30) REVERT: H 260 THR cc_start: 0.8147 (m) cc_final: 0.7852 (t) REVERT: H 305 MET cc_start: 0.6088 (ttp) cc_final: 0.5870 (ttp) REVERT: H 314 GLN cc_start: 0.7482 (tm-30) cc_final: 0.7024 (tm-30) REVERT: H 316 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6907 (mp0) REVERT: H 334 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7097 (mt-10) REVERT: I 16 LEU cc_start: 0.7891 (tp) cc_final: 0.7510 (tp) REVERT: I 82 MET cc_start: 0.6284 (tpp) cc_final: 0.5818 (tpp) REVERT: I 100 GLU cc_start: 0.7668 (tp30) cc_final: 0.7238 (tp30) REVERT: I 107 GLU cc_start: 0.6629 (pm20) cc_final: 0.6185 (pm20) REVERT: I 123 MET cc_start: 0.7133 (mmp) cc_final: 0.6914 (mmp) REVERT: I 133 TYR cc_start: 0.7018 (t80) cc_final: 0.6743 (t80) REVERT: I 215 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8446 (ttmm) REVERT: I 241 GLU cc_start: 0.7237 (tt0) cc_final: 0.7004 (tt0) REVERT: I 247 VAL cc_start: 0.8507 (t) cc_final: 0.8283 (p) REVERT: I 357 ILE cc_start: 0.4680 (OUTLIER) cc_final: 0.4322 (mp) REVERT: N 57 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7270 (mm-30) REVERT: N 111 ASN cc_start: 0.8146 (t0) cc_final: 0.7917 (t0) REVERT: N 154 ASP cc_start: 0.7501 (t0) cc_final: 0.6957 (t0) REVERT: N 195 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6325 (pt0) REVERT: N 238 LYS cc_start: 0.7649 (mmtm) cc_final: 0.7212 (mptt) REVERT: N 244 ASP cc_start: 0.7558 (p0) cc_final: 0.7044 (p0) REVERT: N 279 TYR cc_start: 0.7254 (t80) cc_final: 0.6626 (t80) REVERT: N 282 ILE cc_start: 0.7811 (tt) cc_final: 0.7531 (pt) REVERT: N 313 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6224 (tmm) REVERT: N 350 SER cc_start: 0.8267 (m) cc_final: 0.8011 (p) REVERT: O 44 MET cc_start: 0.4537 (OUTLIER) cc_final: 0.4179 (mtt) REVERT: O 62 ARG cc_start: 0.7889 (ptt-90) cc_final: 0.7612 (ptt-90) REVERT: O 110 LEU cc_start: 0.8413 (mt) cc_final: 0.8176 (mp) REVERT: O 180 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7390 (tt) REVERT: O 216 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6194 (pp) REVERT: O 227 MET cc_start: 0.7791 (mmm) cc_final: 0.7219 (mmm) REVERT: O 259 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7877 (mt-10) REVERT: P 72 GLU cc_start: 0.6291 (mm-30) cc_final: 0.5936 (mm-30) REVERT: P 91 TYR cc_start: 0.8305 (m-80) cc_final: 0.7940 (m-80) REVERT: P 111 ASN cc_start: 0.7352 (m-40) cc_final: 0.7021 (m-40) REVERT: P 123 MET cc_start: 0.7565 (mmm) cc_final: 0.7289 (mmm) REVERT: P 214 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7309 (mt-10) REVERT: P 226 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6978 (mm-30) REVERT: P 313 MET cc_start: 0.6943 (mmm) cc_final: 0.6198 (tmm) REVERT: Q 12 ASN cc_start: 0.8103 (m-40) cc_final: 0.7883 (m110) REVERT: Q 72 GLU cc_start: 0.6401 (tm-30) cc_final: 0.6097 (pp20) REVERT: Q 141 SER cc_start: 0.8232 (m) cc_final: 0.7973 (p) REVERT: Q 149 THR cc_start: 0.8469 (p) cc_final: 0.8263 (p) REVERT: Q 190 MET cc_start: 0.6712 (mtt) cc_final: 0.6454 (mtp) REVERT: Q 214 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6699 (tt0) REVERT: Q 255 PHE cc_start: 0.6436 (p90) cc_final: 0.6231 (p90) REVERT: Q 305 MET cc_start: 0.7121 (mmm) cc_final: 0.6809 (mmm) REVERT: Q 335 ARG cc_start: 0.7304 (mtm110) cc_final: 0.6715 (mtm180) REVERT: R 28 ARG cc_start: 0.8313 (mtp85) cc_final: 0.8053 (mtp-110) REVERT: R 121 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7488 (tm-30) REVERT: S 16 LEU cc_start: 0.7093 (tt) cc_final: 0.6863 (mt) REVERT: S 67 LEU cc_start: 0.7825 (mt) cc_final: 0.7594 (mt) REVERT: S 111 ASN cc_start: 0.7690 (t0) cc_final: 0.7477 (t0) REVERT: S 120 THR cc_start: 0.7502 (m) cc_final: 0.7142 (t) REVERT: S 142 LEU cc_start: 0.7950 (mm) cc_final: 0.7558 (mp) REVERT: S 202 THR cc_start: 0.6742 (OUTLIER) cc_final: 0.5823 (t) REVERT: S 219 VAL cc_start: 0.7872 (p) cc_final: 0.7209 (t) REVERT: S 283 MET cc_start: 0.6775 (mmm) cc_final: 0.6433 (mmm) REVERT: S 304 THR cc_start: 0.6206 (p) cc_final: 0.5938 (p) REVERT: S 316 GLU cc_start: 0.6072 (mt-10) cc_final: 0.5363 (tt0) REVERT: S 325 MET cc_start: 0.6622 (pmm) cc_final: 0.6397 (pmm) REVERT: S 361 GLU cc_start: 0.7030 (pm20) cc_final: 0.6763 (pm20) outliers start: 218 outliers final: 124 residues processed: 1409 average time/residue: 0.6490 time to fit residues: 1535.5037 Evaluate side-chains 1406 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1269 time to evaluate : 5.513 ------------------------------------------------------------------------------- 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 34 CYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 209 ASP 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 B residue 341 LYS Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 26 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 160 VAL 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 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 283 MET Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 360 GLN Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 31 PHE Chi-restraints excluded: chain I residue 215 LYS Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain N residue 225 ASN 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 O residue 44 MET Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 142 LEU Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 260 THR Chi-restraints excluded: chain O residue 299 MET Chi-restraints excluded: chain O residue 358 THR 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 80 ASP Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 165 ILE Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 218 TYR Chi-restraints excluded: chain P residue 299 MET Chi-restraints excluded: chain P residue 305 MET Chi-restraints excluded: chain P residue 330 ILE Chi-restraints excluded: chain P residue 364 GLU 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 80 ASP Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain Q residue 326 LYS Chi-restraints excluded: chain Q residue 370 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 218 TYR Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 300 SER Chi-restraints excluded: chain R residue 351 THR Chi-restraints excluded: chain R residue 361 GLU Chi-restraints excluded: chain R residue 364 GLU Chi-restraints excluded: chain S residue 61 LYS Chi-restraints excluded: chain S residue 80 ASP 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 202 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 298 VAL Chi-restraints excluded: chain d residue 5 CYS Chi-restraints excluded: chain n residue 5 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 569 optimal weight: 0.8980 chunk 387 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 508 optimal weight: 0.8980 chunk 281 optimal weight: 0.9980 chunk 583 optimal weight: 0.6980 chunk 472 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 348 optimal weight: 3.9990 chunk 613 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN B 26 ASN B 269 HIS B 323 GLN C 107 ASN ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 ASN G 129 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN H 360 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 GLN N 115 ASN N 371 HIS O 263 GLN O 353 GLN P 92 ASN P 111 ASN P 137 GLN ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 ASN ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 HIS S 12 ASN S 40 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 51631 Z= 0.206 Angle : 0.659 10.457 70446 Z= 0.323 Chirality : 0.047 0.262 8177 Planarity : 0.004 0.048 9225 Dihedral : 9.083 138.351 8024 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.49 % Allowed : 19.61 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.36 (0.10), residues: 7041 helix: 0.58 (0.10), residues: 2625 sheet: 0.11 (0.17), residues: 936 loop : -0.94 (0.11), residues: 3480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 132 HIS 0.019 0.001 HIS Q 161 PHE 0.026 0.002 PHE B 32 TYR 0.035 0.002 TYR C 3 ARG 0.006 0.001 ARG Q 28 *********************** REFINEMENT MACRO_CYCLE 5 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 1452 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1264 time to evaluate : 5.516 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: A 64 ASP cc_start: 0.8260 (p0) cc_final: 0.8035 (p0) REVERT: A 94 GLU cc_start: 0.7790 (pp20) cc_final: 0.7446 (pp20) REVERT: A 99 LYS cc_start: 0.7861 (mtpp) cc_final: 0.7353 (mtmm) REVERT: A 130 MET cc_start: 0.7932 (mmm) cc_final: 0.7732 (tpp) REVERT: A 133 SER cc_start: 0.8203 (p) cc_final: 0.7921 (p) REVERT: A 135 ASN cc_start: 0.7782 (m110) cc_final: 0.7552 (m-40) REVERT: A 206 GLN cc_start: 0.7862 (tp40) cc_final: 0.7607 (tm-30) REVERT: A 241 GLU cc_start: 0.6336 (mt-10) cc_final: 0.6039 (mt-10) REVERT: A 371 HIS cc_start: 0.7207 (p-80) cc_final: 0.6353 (p-80) REVERT: A 406 SER cc_start: 0.7954 (p) cc_final: 0.7723 (m) REVERT: B 46 LYS cc_start: 0.7801 (tptp) cc_final: 0.7487 (tptp) REVERT: B 57 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7889 (p) REVERT: B 71 ASN cc_start: 0.7099 (p0) cc_final: 0.6887 (p0) REVERT: B 86 LYS cc_start: 0.8313 (ttpp) cc_final: 0.7995 (ttpp) REVERT: B 131 TYR cc_start: 0.7336 (m-10) cc_final: 0.7089 (m-10) REVERT: B 146 LEU cc_start: 0.7539 (mp) cc_final: 0.7176 (mp) REVERT: B 158 ASP cc_start: 0.7234 (t0) cc_final: 0.7004 (t0) REVERT: B 181 ARG cc_start: 0.7275 (ttp80) cc_final: 0.6873 (ttt-90) REVERT: B 195 LYS cc_start: 0.6779 (tppt) cc_final: 0.6576 (tppt) REVERT: B 226 ASN cc_start: 0.8424 (t0) cc_final: 0.7979 (t0) REVERT: B 263 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6396 (mm-30) REVERT: B 272 ASN cc_start: 0.7955 (p0) cc_final: 0.7568 (p0) REVERT: B 320 GLU cc_start: 0.6726 (tp30) cc_final: 0.6322 (tp30) REVERT: B 372 TRP cc_start: 0.6705 (m-90) cc_final: 0.6480 (m-90) REVERT: C 13 CYS cc_start: 0.6841 (t) cc_final: 0.6554 (t) REVERT: C 42 TRP cc_start: 0.8225 (m100) cc_final: 0.7868 (m100) REVERT: C 104 TRP cc_start: 0.7417 (m100) cc_final: 0.6881 (m100) REVERT: C 108 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6839 (mm-30) REVERT: C 138 LYS cc_start: 0.7811 (tttm) cc_final: 0.7382 (tmtm) REVERT: C 209 CYS cc_start: 0.7639 (t) cc_final: 0.7103 (t) REVERT: C 300 GLU cc_start: 0.5934 (tm-30) cc_final: 0.5501 (tm-30) REVERT: C 335 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6646 (mm) REVERT: C 336 SER cc_start: 0.7448 (m) cc_final: 0.7162 (p) REVERT: C 339 LYS cc_start: 0.7623 (mmtp) cc_final: 0.7291 (mmtm) REVERT: D 5 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6630 (tm-30) REVERT: D 42 LEU cc_start: 0.7569 (mm) cc_final: 0.7355 (tp) REVERT: D 43 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6764 (m-10) REVERT: D 119 ASN cc_start: 0.7622 (t0) cc_final: 0.7340 (t0) REVERT: D 158 LYS cc_start: 0.7214 (tppt) cc_final: 0.6952 (mmmt) REVERT: D 163 VAL cc_start: 0.7537 (p) cc_final: 0.7334 (m) REVERT: D 241 ILE cc_start: 0.7968 (mt) cc_final: 0.7675 (tt) REVERT: D 247 PHE cc_start: 0.6522 (t80) cc_final: 0.6121 (t80) REVERT: E 14 LYS cc_start: 0.8352 (mmmt) cc_final: 0.8138 (mmmt) REVERT: E 93 LYS cc_start: 0.8455 (mmmt) cc_final: 0.8139 (mttm) REVERT: E 95 MET cc_start: 0.7795 (mtm) cc_final: 0.7591 (mtm) REVERT: E 123 LYS cc_start: 0.8190 (mmmm) cc_final: 0.7699 (mmmm) REVERT: E 155 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8673 (mmtm) REVERT: F 83 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7318 (mt-10) REVERT: F 95 MET cc_start: 0.5589 (mmp) cc_final: 0.5061 (mmp) REVERT: G 82 VAL cc_start: 0.8502 (t) cc_final: 0.8277 (p) REVERT: G 86 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.6924 (t80) REVERT: G 108 LYS cc_start: 0.8147 (mttp) cc_final: 0.7583 (tttp) REVERT: H 12 ASN cc_start: 0.7042 (p0) cc_final: 0.6689 (p0) REVERT: H 16 LEU cc_start: 0.7154 (mp) cc_final: 0.6773 (mt) REVERT: H 61 LYS cc_start: 0.8342 (mtmm) cc_final: 0.8078 (mtmm) REVERT: H 83 GLU cc_start: 0.7051 (pp20) cc_final: 0.6723 (pp20) REVERT: H 84 LYS cc_start: 0.8137 (mttm) cc_final: 0.7366 (mttm) REVERT: H 123 MET cc_start: 0.7337 (mmp) cc_final: 0.7061 (mmp) REVERT: H 241 GLU cc_start: 0.5759 (tm-30) cc_final: 0.5491 (tm-30) REVERT: H 260 THR cc_start: 0.8168 (m) cc_final: 0.7773 (t) REVERT: H 276 GLU cc_start: 0.7497 (tp30) cc_final: 0.7242 (tp30) REVERT: H 305 MET cc_start: 0.6136 (ttp) cc_final: 0.5604 (ttp) REVERT: H 314 GLN cc_start: 0.7347 (tm-30) cc_final: 0.6821 (tm-30) REVERT: H 316 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6813 (mt-10) REVERT: H 334 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7148 (mt-10) REVERT: H 338 SER cc_start: 0.5535 (OUTLIER) cc_final: 0.4985 (t) REVERT: I 16 LEU cc_start: 0.7580 (tp) cc_final: 0.7143 (mt) REVERT: I 64 ILE cc_start: 0.6310 (pt) cc_final: 0.6009 (tp) REVERT: I 93 GLU cc_start: 0.8238 (tp30) cc_final: 0.7872 (mm-30) REVERT: I 100 GLU cc_start: 0.7647 (tp30) cc_final: 0.7159 (tp30) REVERT: I 107 GLU cc_start: 0.6635 (pm20) cc_final: 0.6296 (pm20) REVERT: I 119 MET cc_start: 0.6596 (mtm) cc_final: 0.6232 (mtm) REVERT: I 133 TYR cc_start: 0.6824 (t80) cc_final: 0.6589 (t80) REVERT: I 176 MET cc_start: 0.3833 (tpt) cc_final: 0.3586 (tpt) REVERT: I 241 GLU cc_start: 0.7068 (tt0) cc_final: 0.6810 (tt0) REVERT: I 248 ILE cc_start: 0.7403 (mm) cc_final: 0.6982 (pt) REVERT: I 254 ARG cc_start: 0.7193 (mtp180) cc_final: 0.6987 (mtp-110) REVERT: I 314 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6570 (tp-100) REVERT: N 111 ASN cc_start: 0.8021 (t0) cc_final: 0.7815 (t0) REVERT: N 154 ASP cc_start: 0.7515 (t0) cc_final: 0.6961 (t0) REVERT: N 176 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6536 (mtt) REVERT: N 195 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6315 (pt0) REVERT: N 238 LYS cc_start: 0.7664 (mmtm) cc_final: 0.6775 (mptt) REVERT: N 240 TYR cc_start: 0.7070 (t80) cc_final: 0.6865 (t80) REVERT: N 244 ASP cc_start: 0.7668 (p0) cc_final: 0.7306 (p0) REVERT: N 282 ILE cc_start: 0.7558 (tt) cc_final: 0.7302 (pt) REVERT: N 350 SER cc_start: 0.8186 (m) cc_final: 0.7879 (p) REVERT: O 106 THR cc_start: 0.7380 (m) cc_final: 0.7099 (p) REVERT: O 110 LEU cc_start: 0.8256 (mt) cc_final: 0.7999 (mp) REVERT: O 216 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.5956 (pp) REVERT: O 227 MET cc_start: 0.7721 (mmm) cc_final: 0.7128 (mmm) REVERT: O 259 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7994 (tp30) REVERT: O 313 MET cc_start: 0.6595 (mmm) cc_final: 0.6366 (tpp) REVERT: O 326 LYS cc_start: 0.6937 (pttm) cc_final: 0.6666 (mmmt) REVERT: O 335 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7884 (ptt-90) REVERT: P 72 GLU cc_start: 0.6088 (mm-30) cc_final: 0.5837 (mm-30) REVERT: P 111 ASN cc_start: 0.7454 (m110) cc_final: 0.7165 (m-40) REVERT: P 123 MET cc_start: 0.7528 (mmm) cc_final: 0.7289 (tpp) REVERT: P 161 HIS cc_start: 0.7383 (p90) cc_final: 0.7053 (p-80) REVERT: P 176 MET cc_start: 0.7060 (mtt) cc_final: 0.6605 (mmm) REVERT: P 195 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.6168 (pt0) REVERT: P 214 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7091 (mt-10) REVERT: P 226 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6967 (mm-30) REVERT: P 313 MET cc_start: 0.6772 (mmm) cc_final: 0.6099 (tmm) REVERT: P 335 ARG cc_start: 0.8348 (mtm180) cc_final: 0.8074 (mpp80) REVERT: Q 149 THR cc_start: 0.8421 (p) cc_final: 0.8135 (p) REVERT: Q 153 LEU cc_start: 0.7160 (tp) cc_final: 0.6841 (tp) REVERT: Q 190 MET cc_start: 0.6576 (mtt) cc_final: 0.6351 (mtp) REVERT: Q 214 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6646 (tt0) REVERT: Q 284 LYS cc_start: 0.7421 (mtpp) cc_final: 0.7079 (mtmm) REVERT: Q 305 MET cc_start: 0.7044 (mmm) cc_final: 0.6622 (mmm) REVERT: Q 335 ARG cc_start: 0.7425 (mtm110) cc_final: 0.6412 (mtm180) REVERT: R 28 ARG cc_start: 0.8255 (mtp85) cc_final: 0.8040 (mtp-110) REVERT: R 121 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7519 (tm-30) REVERT: R 177 ARG cc_start: 0.7762 (ttt-90) cc_final: 0.7433 (ttt-90) REVERT: R 248 ILE cc_start: 0.8054 (mm) cc_final: 0.7511 (tp) REVERT: R 283 MET cc_start: 0.6661 (mmt) cc_final: 0.6452 (tpp) REVERT: S 16 LEU cc_start: 0.7007 (tt) cc_final: 0.6774 (mt) REVERT: S 67 LEU cc_start: 0.7763 (mt) cc_final: 0.7509 (mt) REVERT: S 120 THR cc_start: 0.7332 (m) cc_final: 0.7085 (t) REVERT: S 176 MET cc_start: 0.6860 (mmm) cc_final: 0.6396 (mmm) REVERT: S 192 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.6282 (pt) REVERT: S 195 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6143 (pt0) REVERT: S 202 THR cc_start: 0.6697 (OUTLIER) cc_final: 0.6402 (t) REVERT: S 253 GLU cc_start: 0.7592 (tp30) cc_final: 0.7293 (mm-30) REVERT: S 283 MET cc_start: 0.6724 (mmm) cc_final: 0.6419 (mmm) REVERT: S 304 THR cc_start: 0.6052 (p) cc_final: 0.5739 (p) outliers start: 188 outliers final: 117 residues processed: 1339 average time/residue: 0.6195 time to fit residues: 1384.9591 Evaluate side-chains 1356 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1225 time to evaluate : 5.247 ------------------------------------------------------------------------------- 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 51 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 269 HIS Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain C residue 26 CYS Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain G residue 86 PHE 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 159 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 283 MET Chi-restraints excluded: chain H residue 289 ILE Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 31 PHE Chi-restraints excluded: chain I residue 215 LYS Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 311 ASP Chi-restraints excluded: chain I residue 314 GLN Chi-restraints excluded: chain I residue 325 MET Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 176 MET Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain N residue 291 LYS Chi-restraints excluded: chain N residue 313 MET Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain O residue 142 LEU Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 260 THR Chi-restraints excluded: chain O residue 293 LEU Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 335 ARG Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 80 ASP 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 305 MET Chi-restraints excluded: chain P residue 373 LYS Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 165 ILE Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain Q residue 326 LYS Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain Q residue 339 VAL Chi-restraints excluded: chain Q residue 341 ILE Chi-restraints excluded: chain R residue 61 LYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 351 THR Chi-restraints excluded: chain R residue 364 GLU Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 61 LYS Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain S residue 202 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain n residue 5 CYS Chi-restraints excluded: chain o residue 5 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 229 optimal weight: 2.9990 chunk 615 optimal weight: 1.9990 chunk 135 optimal weight: 0.0020 chunk 401 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 684 optimal weight: 50.0000 chunk 567 optimal weight: 2.9990 chunk 316 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 226 optimal weight: 0.1980 chunk 359 optimal weight: 9.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS B 370 ASN ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 ASN I 92 ASN I 353 GLN O 111 ASN O 371 HIS ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 HIS ** S 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 51631 Z= 0.213 Angle : 0.647 11.205 70446 Z= 0.316 Chirality : 0.047 0.307 8177 Planarity : 0.004 0.054 9225 Dihedral : 8.811 142.270 8023 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.56 % Allowed : 21.17 % Favored : 74.27 % 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: -0.25 (0.10), residues: 7041 helix: 0.75 (0.10), residues: 2614 sheet: -0.14 (0.16), residues: 1090 loop : -0.86 (0.11), residues: 3337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP n 1 HIS 0.025 0.001 HIS P 275 PHE 0.026 0.002 PHE D 185 TYR 0.024 0.001 TYR O 166 ARG 0.007 0.000 ARG P 206 *********************** REFINEMENT MACRO_CYCLE 6 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 1430 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1239 time to evaluate : 5.542 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: A 64 ASP cc_start: 0.8258 (p0) cc_final: 0.8017 (p0) REVERT: A 94 GLU cc_start: 0.7747 (pp20) cc_final: 0.7422 (pp20) REVERT: A 99 LYS cc_start: 0.7885 (mtpp) cc_final: 0.7485 (mtmm) REVERT: A 130 MET cc_start: 0.7898 (mmm) cc_final: 0.7631 (tpp) REVERT: A 133 SER cc_start: 0.8240 (p) cc_final: 0.7984 (p) REVERT: A 135 ASN cc_start: 0.7810 (m110) cc_final: 0.7517 (m-40) REVERT: A 206 GLN cc_start: 0.7893 (tp40) cc_final: 0.7640 (tm-30) REVERT: A 241 GLU cc_start: 0.6441 (mt-10) cc_final: 0.6189 (mt-10) REVERT: A 294 GLN cc_start: 0.8032 (tt0) cc_final: 0.7728 (tt0) REVERT: A 371 HIS cc_start: 0.7193 (p-80) cc_final: 0.6291 (p-80) REVERT: A 406 SER cc_start: 0.7967 (p) cc_final: 0.7718 (m) REVERT: B 46 LYS cc_start: 0.7820 (tptp) cc_final: 0.7453 (tptp) REVERT: B 57 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7918 (p) REVERT: B 86 LYS cc_start: 0.8335 (ttpp) cc_final: 0.7999 (ttpp) REVERT: B 106 LYS cc_start: 0.8123 (mmtm) cc_final: 0.7922 (mmmt) REVERT: B 146 LEU cc_start: 0.7510 (mp) cc_final: 0.7187 (mp) REVERT: B 181 ARG cc_start: 0.7331 (ttp80) cc_final: 0.6944 (ttt-90) REVERT: B 195 LYS cc_start: 0.6815 (tppt) cc_final: 0.6574 (tppt) REVERT: B 226 ASN cc_start: 0.8488 (t0) cc_final: 0.8234 (t0) REVERT: B 263 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6423 (mm-30) REVERT: B 320 GLU cc_start: 0.6774 (tp30) cc_final: 0.6456 (tp30) REVERT: B 377 GLU cc_start: 0.7434 (mp0) cc_final: 0.7102 (mp0) REVERT: C 13 CYS cc_start: 0.6854 (t) cc_final: 0.6531 (t) REVERT: C 42 TRP cc_start: 0.8225 (m100) cc_final: 0.7837 (m100) REVERT: C 104 TRP cc_start: 0.7433 (m100) cc_final: 0.6341 (m100) REVERT: C 108 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6300 (tp30) REVERT: C 138 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7297 (tmtm) REVERT: C 209 CYS cc_start: 0.7745 (t) cc_final: 0.7334 (t) REVERT: C 300 GLU cc_start: 0.6018 (tm-30) cc_final: 0.5548 (tm-30) REVERT: C 301 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7613 (ttm110) REVERT: C 335 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6691 (mm) REVERT: C 336 SER cc_start: 0.7395 (m) cc_final: 0.7127 (p) REVERT: C 339 LYS cc_start: 0.7692 (mmtp) cc_final: 0.7408 (mmtm) REVERT: D 5 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6646 (tm-30) REVERT: D 42 LEU cc_start: 0.7644 (mm) cc_final: 0.7414 (tp) REVERT: D 43 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6748 (m-10) REVERT: D 119 ASN cc_start: 0.7634 (t0) cc_final: 0.7310 (t0) REVERT: D 241 ILE cc_start: 0.7985 (mt) cc_final: 0.7691 (tt) REVERT: D 247 PHE cc_start: 0.6527 (t80) cc_final: 0.6069 (t80) REVERT: D 266 MET cc_start: 0.7372 (ptp) cc_final: 0.7010 (ptp) REVERT: E 14 LYS cc_start: 0.8336 (mmmt) cc_final: 0.8123 (mmmt) REVERT: E 93 LYS cc_start: 0.8472 (mmmt) cc_final: 0.8141 (mttm) REVERT: E 95 MET cc_start: 0.7806 (mtm) cc_final: 0.7593 (mtm) REVERT: E 123 LYS cc_start: 0.8127 (mmmm) cc_final: 0.7797 (mmmm) REVERT: E 155 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8660 (mmtm) REVERT: G 82 VAL cc_start: 0.8406 (t) cc_final: 0.8193 (p) REVERT: G 86 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7068 (t80) REVERT: G 108 LYS cc_start: 0.8191 (mttp) cc_final: 0.7654 (tttp) REVERT: G 131 LYS cc_start: 0.8320 (mmtm) cc_final: 0.8077 (mmmm) REVERT: H 12 ASN cc_start: 0.6998 (p0) cc_final: 0.6722 (p0) REVERT: H 16 LEU cc_start: 0.6972 (mp) cc_final: 0.6538 (mt) REVERT: H 61 LYS cc_start: 0.8329 (mtmm) cc_final: 0.8110 (mtmm) REVERT: H 83 GLU cc_start: 0.7106 (pp20) cc_final: 0.6724 (pp20) REVERT: H 84 LYS cc_start: 0.8172 (mttm) cc_final: 0.7393 (mttm) REVERT: H 121 GLN cc_start: 0.8131 (pp30) cc_final: 0.7872 (pp30) REVERT: H 123 MET cc_start: 0.7359 (mmp) cc_final: 0.7055 (mmp) REVERT: H 221 LEU cc_start: 0.7890 (tt) cc_final: 0.7682 (tp) REVERT: H 241 GLU cc_start: 0.5770 (tm-30) cc_final: 0.5540 (tm-30) REVERT: H 305 MET cc_start: 0.6293 (ttp) cc_final: 0.5713 (ttp) REVERT: H 314 GLN cc_start: 0.7408 (tm-30) cc_final: 0.6818 (tm-30) REVERT: H 338 SER cc_start: 0.5509 (OUTLIER) cc_final: 0.4912 (t) REVERT: I 16 LEU cc_start: 0.7449 (tp) cc_final: 0.7015 (mt) REVERT: I 64 ILE cc_start: 0.6333 (pt) cc_final: 0.6059 (tp) REVERT: I 88 HIS cc_start: 0.7603 (t-170) cc_final: 0.7131 (t-170) REVERT: I 92 ASN cc_start: 0.8054 (m110) cc_final: 0.7521 (m-40) REVERT: I 100 GLU cc_start: 0.7649 (tp30) cc_final: 0.7139 (tp30) REVERT: I 107 GLU cc_start: 0.6676 (pm20) cc_final: 0.6324 (pm20) REVERT: I 121 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7881 (tm-30) REVERT: I 176 MET cc_start: 0.3789 (tpt) cc_final: 0.3583 (tpt) REVERT: I 241 GLU cc_start: 0.7110 (tt0) cc_final: 0.6817 (tt0) REVERT: I 248 ILE cc_start: 0.7472 (mm) cc_final: 0.7077 (pt) REVERT: I 314 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6539 (tp-100) REVERT: I 316 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7752 (mm-30) REVERT: N 72 GLU cc_start: 0.6892 (tp30) cc_final: 0.6508 (mp0) REVERT: N 111 ASN cc_start: 0.8044 (t0) cc_final: 0.7834 (t0) REVERT: N 154 ASP cc_start: 0.7494 (t0) cc_final: 0.6921 (t0) REVERT: N 195 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6321 (pt0) REVERT: N 238 LYS cc_start: 0.7659 (mmtm) cc_final: 0.6674 (mptt) REVERT: N 244 ASP cc_start: 0.7666 (p0) cc_final: 0.7287 (p0) REVERT: N 282 ILE cc_start: 0.7567 (tt) cc_final: 0.7314 (pt) REVERT: N 350 SER cc_start: 0.8225 (m) cc_final: 0.7928 (p) REVERT: O 41 GLN cc_start: 0.6395 (OUTLIER) cc_final: 0.6047 (mp10) REVERT: O 106 THR cc_start: 0.7308 (m) cc_final: 0.7052 (p) REVERT: O 216 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.5964 (pp) REVERT: O 227 MET cc_start: 0.7763 (mmm) cc_final: 0.7105 (mmm) REVERT: O 259 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8032 (tp30) REVERT: O 304 THR cc_start: 0.7510 (OUTLIER) cc_final: 0.7217 (m) REVERT: O 313 MET cc_start: 0.6612 (mmm) cc_final: 0.6321 (tpp) REVERT: O 326 LYS cc_start: 0.6981 (pttm) cc_final: 0.6662 (mmmt) REVERT: O 335 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7889 (ptt-90) REVERT: P 47 MET cc_start: 0.4244 (mmt) cc_final: 0.3690 (mtt) REVERT: P 72 GLU cc_start: 0.6063 (mm-30) cc_final: 0.5776 (mm-30) REVERT: P 84 LYS cc_start: 0.7612 (ttmm) cc_final: 0.7364 (mttp) REVERT: P 111 ASN cc_start: 0.7474 (m110) cc_final: 0.7190 (m-40) REVERT: P 161 HIS cc_start: 0.7314 (p90) cc_final: 0.6974 (p-80) REVERT: P 176 MET cc_start: 0.7104 (mtt) cc_final: 0.6621 (mmm) REVERT: P 195 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6194 (pt0) REVERT: P 214 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7279 (mt-10) REVERT: P 226 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7026 (mm-30) REVERT: P 313 MET cc_start: 0.6547 (tmm) cc_final: 0.5812 (tmm) REVERT: P 335 ARG cc_start: 0.8462 (mtm180) cc_final: 0.8125 (mpp80) REVERT: Q 105 LEU cc_start: 0.7940 (mm) cc_final: 0.7730 (mp) REVERT: Q 153 LEU cc_start: 0.7158 (tp) cc_final: 0.6861 (tp) REVERT: Q 159 VAL cc_start: 0.7669 (t) cc_final: 0.7392 (m) REVERT: Q 190 MET cc_start: 0.6635 (mtt) cc_final: 0.6429 (mtp) REVERT: Q 284 LYS cc_start: 0.7517 (mtpp) cc_final: 0.7315 (mtmm) REVERT: Q 305 MET cc_start: 0.7008 (mmm) cc_final: 0.6287 (mmm) REVERT: Q 335 ARG cc_start: 0.7394 (mtm110) cc_final: 0.6407 (mtm180) REVERT: R 28 ARG cc_start: 0.8291 (mtp85) cc_final: 0.8072 (mtp-110) REVERT: R 121 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7469 (tm-30) REVERT: R 248 ILE cc_start: 0.8014 (mm) cc_final: 0.7658 (tp) REVERT: R 283 MET cc_start: 0.6664 (mmt) cc_final: 0.5884 (tpp) REVERT: R 290 ARG cc_start: 0.6391 (mtp180) cc_final: 0.6178 (mtp180) REVERT: S 16 LEU cc_start: 0.7041 (tt) cc_final: 0.6728 (mt) REVERT: S 120 THR cc_start: 0.7365 (m) cc_final: 0.7127 (t) REVERT: S 152 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8196 (m) REVERT: S 176 MET cc_start: 0.7100 (mmm) cc_final: 0.6793 (mmm) REVERT: S 195 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6260 (pt0) REVERT: S 201 VAL cc_start: 0.6922 (OUTLIER) cc_final: 0.6629 (t) REVERT: S 253 GLU cc_start: 0.7608 (tp30) cc_final: 0.7180 (tp30) REVERT: S 283 MET cc_start: 0.6779 (mmm) cc_final: 0.6121 (mmm) REVERT: S 304 THR cc_start: 0.5972 (p) cc_final: 0.5719 (p) REVERT: S 361 GLU cc_start: 0.7182 (pm20) cc_final: 0.6938 (pm20) outliers start: 191 outliers final: 140 residues processed: 1322 average time/residue: 0.5941 time to fit residues: 1311.7700 Evaluate side-chains 1369 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1213 time to evaluate : 5.335 ------------------------------------------------------------------------------- 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 21 TYR Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 269 HIS Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain G residue 86 PHE 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 159 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 283 MET Chi-restraints excluded: chain H residue 289 ILE Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 299 MET Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 31 PHE Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 215 LYS Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 311 ASP Chi-restraints excluded: chain I residue 314 GLN Chi-restraints excluded: chain I residue 325 MET Chi-restraints excluded: chain I residue 353 GLN Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 176 MET Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 291 LYS 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 O residue 41 GLN Chi-restraints excluded: chain O residue 94 LEU 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 175 ILE Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 260 THR Chi-restraints excluded: chain O residue 294 TYR Chi-restraints excluded: chain O residue 299 MET Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 335 ARG Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 80 ASP 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 195 GLU Chi-restraints excluded: chain P residue 373 LYS Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain Q residue 326 LYS Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain Q residue 339 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 218 TYR Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 351 THR Chi-restraints excluded: chain R residue 361 GLU Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain e residue 5 CYS Chi-restraints excluded: chain h residue 5 CYS Chi-restraints excluded: chain n residue 5 CYS Chi-restraints excluded: chain o residue 5 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 659 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 389 optimal weight: 5.9990 chunk 499 optimal weight: 2.9990 chunk 387 optimal weight: 6.9990 chunk 575 optimal weight: 0.9980 chunk 381 optimal weight: 8.9990 chunk 681 optimal weight: 6.9990 chunk 426 optimal weight: 2.9990 chunk 415 optimal weight: 9.9990 chunk 314 optimal weight: 50.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN B 205 ASN ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 HIS ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 GLN I 88 HIS ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 353 GLN P 137 GLN ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.152 51631 Z= 0.483 Angle : 0.823 14.461 70446 Z= 0.420 Chirality : 0.053 0.361 8177 Planarity : 0.006 0.068 9225 Dihedral : 9.524 147.522 8023 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.16 % Favored : 92.79 % Rotamer: Outliers : 5.83 % Allowed : 21.38 % Favored : 72.79 % 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: -0.93 (0.10), residues: 7041 helix: 0.11 (0.10), residues: 2621 sheet: -0.47 (0.16), residues: 1093 loop : -1.21 (0.11), residues: 3327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP n 1 HIS 0.021 0.002 HIS P 275 PHE 0.036 0.003 PHE A 331 TYR 0.040 0.003 TYR R 218 ARG 0.008 0.001 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 7 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 1525 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1281 time to evaluate : 5.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.7056 (mmm) cc_final: 0.6735 (mmt) REVERT: A 94 GLU cc_start: 0.7785 (pp20) cc_final: 0.7530 (pp20) REVERT: A 99 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7544 (mtmm) REVERT: A 107 ASP cc_start: 0.7713 (t0) cc_final: 0.7342 (t0) REVERT: A 130 MET cc_start: 0.7987 (mmm) cc_final: 0.7308 (mmp) REVERT: A 132 GLU cc_start: 0.7884 (tt0) cc_final: 0.7673 (tt0) REVERT: A 135 ASN cc_start: 0.7774 (m110) cc_final: 0.7473 (m-40) REVERT: A 206 GLN cc_start: 0.7980 (tp40) cc_final: 0.7734 (tm-30) REVERT: A 294 GLN cc_start: 0.8045 (tt0) cc_final: 0.7693 (tt0) REVERT: A 371 HIS cc_start: 0.7215 (p-80) cc_final: 0.6296 (p-80) REVERT: A 406 SER cc_start: 0.8022 (p) cc_final: 0.7782 (m) REVERT: B 46 LYS cc_start: 0.7850 (tptp) cc_final: 0.7489 (tptp) REVERT: B 57 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7918 (p) REVERT: B 86 LYS cc_start: 0.8433 (ttpp) cc_final: 0.8139 (ttpp) REVERT: B 146 LEU cc_start: 0.7969 (mp) cc_final: 0.7642 (mp) REVERT: B 181 ARG cc_start: 0.7266 (ttp80) cc_final: 0.6931 (ttt-90) REVERT: B 226 ASN cc_start: 0.8551 (t0) cc_final: 0.8058 (t0) REVERT: B 263 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6523 (tp30) REVERT: B 320 GLU cc_start: 0.6971 (tp30) cc_final: 0.6701 (tp30) REVERT: B 377 GLU cc_start: 0.7522 (mp0) cc_final: 0.7250 (mp0) REVERT: C 13 CYS cc_start: 0.6917 (t) cc_final: 0.6626 (t) REVERT: C 31 GLU cc_start: 0.7174 (pt0) cc_final: 0.6872 (tt0) REVERT: C 42 TRP cc_start: 0.8311 (m100) cc_final: 0.7959 (m100) REVERT: C 90 LEU cc_start: 0.8206 (tp) cc_final: 0.7978 (mt) REVERT: C 104 TRP cc_start: 0.7457 (m100) cc_final: 0.6701 (m100) REVERT: C 108 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6760 (mm-30) REVERT: C 138 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7344 (tmtm) REVERT: C 156 LEU cc_start: 0.8203 (mt) cc_final: 0.8001 (mp) REVERT: C 196 PHE cc_start: 0.5680 (OUTLIER) cc_final: 0.4496 (p90) REVERT: C 197 GLU cc_start: 0.5597 (tt0) cc_final: 0.5370 (mt-10) REVERT: C 209 CYS cc_start: 0.7762 (t) cc_final: 0.7363 (t) REVERT: C 300 GLU cc_start: 0.6310 (tm-30) cc_final: 0.5824 (tm-30) REVERT: C 301 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7711 (ttm110) REVERT: C 335 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6864 (mm) REVERT: C 336 SER cc_start: 0.7678 (m) cc_final: 0.7355 (p) REVERT: D 5 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6694 (tm-30) REVERT: D 43 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6787 (m-10) REVERT: D 119 ASN cc_start: 0.7744 (t0) cc_final: 0.7428 (t0) REVERT: D 241 ILE cc_start: 0.8051 (mt) cc_final: 0.7799 (tt) REVERT: D 245 HIS cc_start: 0.7245 (t70) cc_final: 0.7025 (t70) REVERT: D 247 PHE cc_start: 0.6820 (t80) cc_final: 0.6440 (t80) REVERT: D 265 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7736 (ttm110) REVERT: E 14 LYS cc_start: 0.8358 (mmmt) cc_final: 0.8147 (mmmt) REVERT: E 18 ASN cc_start: 0.7673 (t0) cc_final: 0.7406 (t0) REVERT: E 93 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8184 (mttm) REVERT: E 155 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8667 (mmtm) REVERT: F 91 MET cc_start: 0.8342 (mmm) cc_final: 0.7446 (mmm) REVERT: F 115 SER cc_start: 0.8762 (p) cc_final: 0.8481 (m) REVERT: G 82 VAL cc_start: 0.8562 (t) cc_final: 0.8361 (p) REVERT: G 86 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.6647 (t80) REVERT: G 90 ASP cc_start: 0.8057 (t70) cc_final: 0.7400 (t70) REVERT: G 108 LYS cc_start: 0.8236 (mttp) cc_final: 0.7729 (tttp) REVERT: H 12 ASN cc_start: 0.7206 (p0) cc_final: 0.6870 (p0) REVERT: H 61 LYS cc_start: 0.8468 (mtmm) cc_final: 0.8185 (mtmm) REVERT: H 83 GLU cc_start: 0.7183 (pp20) cc_final: 0.6862 (pp20) REVERT: H 84 LYS cc_start: 0.8274 (mttm) cc_final: 0.7436 (mttm) REVERT: H 121 GLN cc_start: 0.8006 (pp30) cc_final: 0.7683 (pp30) REVERT: H 154 ASP cc_start: 0.6544 (t70) cc_final: 0.6198 (t70) REVERT: H 221 LEU cc_start: 0.8215 (tt) cc_final: 0.7967 (tp) REVERT: H 222 ASP cc_start: 0.7105 (t0) cc_final: 0.6651 (t0) REVERT: H 241 GLU cc_start: 0.5758 (tm-30) cc_final: 0.5547 (tm-30) REVERT: H 305 MET cc_start: 0.6291 (ttp) cc_final: 0.5817 (ttp) REVERT: H 314 GLN cc_start: 0.7565 (tm-30) cc_final: 0.7062 (tm-30) REVERT: H 338 SER cc_start: 0.5631 (OUTLIER) cc_final: 0.5173 (t) REVERT: I 43 VAL cc_start: 0.7373 (p) cc_final: 0.7030 (m) REVERT: I 100 GLU cc_start: 0.7538 (tp30) cc_final: 0.7083 (tp30) REVERT: I 107 GLU cc_start: 0.6750 (pm20) cc_final: 0.6537 (pm20) REVERT: I 121 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8001 (tm-30) REVERT: I 176 MET cc_start: 0.3955 (tpt) cc_final: 0.3742 (tpt) REVERT: I 189 LEU cc_start: 0.7642 (tp) cc_final: 0.7427 (tp) REVERT: I 193 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5570 (tp) REVERT: I 241 GLU cc_start: 0.7249 (tt0) cc_final: 0.6941 (tt0) REVERT: I 314 GLN cc_start: 0.7217 (tp-100) cc_final: 0.6874 (tp-100) REVERT: I 316 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7494 (mm-30) REVERT: N 136 ILE cc_start: 0.7195 (mp) cc_final: 0.6780 (mm) REVERT: N 154 ASP cc_start: 0.7491 (t0) cc_final: 0.7003 (t0) REVERT: N 244 ASP cc_start: 0.7549 (p0) cc_final: 0.7173 (p0) REVERT: N 279 TYR cc_start: 0.7363 (t80) cc_final: 0.6765 (t80) REVERT: N 282 ILE cc_start: 0.7787 (tt) cc_final: 0.7540 (pt) REVERT: N 313 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6229 (tmm) REVERT: N 350 SER cc_start: 0.8393 (m) cc_final: 0.8083 (p) REVERT: O 106 THR cc_start: 0.7404 (m) cc_final: 0.7097 (p) REVERT: O 141 SER cc_start: 0.8045 (m) cc_final: 0.7805 (t) REVERT: O 216 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6317 (pp) REVERT: O 227 MET cc_start: 0.7676 (mmm) cc_final: 0.7192 (mmm) REVERT: O 259 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8121 (tp30) REVERT: O 282 ILE cc_start: 0.8436 (tt) cc_final: 0.8230 (tt) REVERT: O 305 MET cc_start: 0.7768 (mtt) cc_final: 0.7557 (mtt) REVERT: O 313 MET cc_start: 0.6937 (mmm) cc_final: 0.6545 (tpt) REVERT: O 335 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8016 (ptt-90) REVERT: P 47 MET cc_start: 0.4227 (mmt) cc_final: 0.3694 (mtt) REVERT: P 72 GLU cc_start: 0.6328 (mm-30) cc_final: 0.6022 (mm-30) REVERT: P 76 ILE cc_start: 0.7733 (mm) cc_final: 0.7388 (mt) REVERT: P 111 ASN cc_start: 0.7447 (m110) cc_final: 0.7171 (m-40) REVERT: P 123 MET cc_start: 0.7524 (tpp) cc_final: 0.7312 (mmm) REVERT: P 176 MET cc_start: 0.7054 (mtt) cc_final: 0.6643 (mmm) REVERT: P 214 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7354 (mt-10) REVERT: P 226 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7089 (mm-30) REVERT: P 275 HIS cc_start: 0.7110 (p-80) cc_final: 0.6539 (p-80) REVERT: P 313 MET cc_start: 0.6824 (tmm) cc_final: 0.6241 (tmm) REVERT: P 317 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7426 (tp) REVERT: P 335 ARG cc_start: 0.8557 (mtm180) cc_final: 0.8218 (mpp80) REVERT: P 361 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6366 (mm-30) REVERT: Q 72 GLU cc_start: 0.6656 (tm-30) cc_final: 0.6245 (pt0) REVERT: Q 149 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.8113 (p) REVERT: Q 153 LEU cc_start: 0.7303 (tp) cc_final: 0.7090 (tp) REVERT: Q 190 MET cc_start: 0.6701 (mtt) cc_final: 0.6394 (mtp) REVERT: Q 261 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8592 (mp) REVERT: Q 284 LYS cc_start: 0.7751 (mtpp) cc_final: 0.7481 (mtmm) REVERT: Q 335 ARG cc_start: 0.7513 (mtm110) cc_final: 0.6971 (mtm180) REVERT: Q 360 GLN cc_start: 0.7456 (tp40) cc_final: 0.7041 (tp40) REVERT: R 57 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7087 (mm-30) REVERT: R 85 ILE cc_start: 0.8395 (tt) cc_final: 0.8098 (tp) REVERT: R 121 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7502 (tm-30) REVERT: R 143 TYR cc_start: 0.7959 (m-80) cc_final: 0.7683 (m-80) REVERT: R 177 ARG cc_start: 0.7833 (ttt-90) cc_final: 0.7588 (ttt-90) REVERT: R 207 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7103 (mm-30) REVERT: R 229 THR cc_start: 0.8053 (m) cc_final: 0.7844 (t) REVERT: R 235 SER cc_start: 0.8352 (p) cc_final: 0.7934 (t) REVERT: R 238 LYS cc_start: 0.8470 (tppt) cc_final: 0.8120 (mmtm) REVERT: S 16 LEU cc_start: 0.7086 (tt) cc_final: 0.6683 (mp) REVERT: S 82 MET cc_start: 0.7099 (tpt) cc_final: 0.6877 (tpt) REVERT: S 120 THR cc_start: 0.7375 (m) cc_final: 0.7143 (t) REVERT: S 195 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6339 (pt0) REVERT: S 201 VAL cc_start: 0.7406 (OUTLIER) cc_final: 0.7167 (t) REVERT: S 253 GLU cc_start: 0.7728 (tp30) cc_final: 0.7279 (tp30) REVERT: S 325 MET cc_start: 0.6630 (pmm) cc_final: 0.6402 (pmm) outliers start: 244 outliers final: 174 residues processed: 1381 average time/residue: 0.6092 time to fit residues: 1408.7261 Evaluate side-chains 1443 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1253 time to evaluate : 5.577 ------------------------------------------------------------------------------- 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 21 TYR Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 26 CYS Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 162 CYS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 283 MET Chi-restraints excluded: chain H residue 289 ILE Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 299 MET Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 360 GLN Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 31 PHE Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 325 MET Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 176 MET Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 194 THR Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain N residue 225 ASN Chi-restraints excluded: chain N residue 291 LYS 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 351 THR Chi-restraints excluded: chain N residue 357 ILE Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 142 LEU Chi-restraints excluded: chain O residue 166 TYR Chi-restraints excluded: chain O residue 175 ILE Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 260 THR Chi-restraints excluded: chain O residue 294 TYR Chi-restraints excluded: chain O residue 299 MET Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 335 ARG 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 80 ASP 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 190 MET Chi-restraints excluded: chain P residue 218 TYR Chi-restraints excluded: chain P residue 317 ILE Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain P residue 373 LYS Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain Q residue 261 LEU Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain Q residue 326 LYS Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 339 VAL Chi-restraints excluded: chain Q residue 341 ILE Chi-restraints excluded: chain Q residue 370 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 218 TYR Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 351 THR Chi-restraints excluded: chain R residue 361 GLU Chi-restraints excluded: chain R residue 364 GLU Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 75 ILE Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain e residue 5 CYS Chi-restraints excluded: chain h residue 5 CYS Chi-restraints excluded: chain o residue 5 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 421 optimal weight: 0.0980 chunk 272 optimal weight: 20.0000 chunk 406 optimal weight: 0.2980 chunk 205 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 433 optimal weight: 1.9990 chunk 464 optimal weight: 0.6980 chunk 336 optimal weight: 30.0000 chunk 63 optimal weight: 2.9990 chunk 535 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN B 269 HIS ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 HIS ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN ** D 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN I 59 GLN ** N 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 115 ASN ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 ASN R 173 HIS ** S 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 51631 Z= 0.197 Angle : 0.666 13.903 70446 Z= 0.327 Chirality : 0.047 0.325 8177 Planarity : 0.004 0.059 9225 Dihedral : 8.808 148.653 8022 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.16 % Allowed : 24.58 % Favored : 71.26 % 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: -0.56 (0.10), residues: 7041 helix: 0.50 (0.10), residues: 2694 sheet: -0.35 (0.16), residues: 1089 loop : -1.07 (0.11), residues: 3258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 132 HIS 0.015 0.001 HIS D 254 PHE 0.027 0.002 PHE F 25 TYR 0.021 0.001 TYR S 279 ARG 0.007 0.000 ARG P 206 *********************** REFINEMENT MACRO_CYCLE 8 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 1420 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1246 time to evaluate : 5.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.6977 (mmm) cc_final: 0.6659 (mmt) REVERT: A 55 VAL cc_start: 0.7854 (t) cc_final: 0.7432 (p) REVERT: A 94 GLU cc_start: 0.7698 (pp20) cc_final: 0.7372 (pp20) REVERT: A 99 LYS cc_start: 0.7828 (mtpp) cc_final: 0.7296 (mtmm) REVERT: A 104 GLU cc_start: 0.7753 (mp0) cc_final: 0.7419 (mp0) REVERT: A 130 MET cc_start: 0.7791 (mmm) cc_final: 0.7175 (mpp) REVERT: A 132 GLU cc_start: 0.7827 (tt0) cc_final: 0.7623 (tt0) REVERT: A 135 ASN cc_start: 0.7808 (m110) cc_final: 0.7486 (m-40) REVERT: A 294 GLN cc_start: 0.7922 (tt0) cc_final: 0.7500 (tt0) REVERT: A 371 HIS cc_start: 0.7263 (p-80) cc_final: 0.6273 (p-80) REVERT: A 372 MET cc_start: 0.6747 (tpp) cc_final: 0.6382 (ppp) REVERT: A 406 SER cc_start: 0.7989 (p) cc_final: 0.7718 (m) REVERT: B 7 LYS cc_start: 0.8367 (ttmt) cc_final: 0.8095 (ptmt) REVERT: B 46 LYS cc_start: 0.7815 (tptp) cc_final: 0.7467 (tptp) REVERT: B 57 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7897 (p) REVERT: B 86 LYS cc_start: 0.8360 (ttpp) cc_final: 0.8079 (ttpp) REVERT: B 105 CYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7038 (m) REVERT: B 146 LEU cc_start: 0.7540 (mp) cc_final: 0.7203 (mp) REVERT: B 181 ARG cc_start: 0.7279 (ttp80) cc_final: 0.6874 (ttt-90) REVERT: B 195 LYS cc_start: 0.6735 (tppt) cc_final: 0.6469 (tppt) REVERT: B 226 ASN cc_start: 0.8499 (t0) cc_final: 0.8264 (t0) REVERT: B 263 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6342 (tp30) REVERT: B 320 GLU cc_start: 0.6753 (tp30) cc_final: 0.6520 (tp30) REVERT: C 13 CYS cc_start: 0.6867 (t) cc_final: 0.6597 (t) REVERT: C 23 ILE cc_start: 0.7453 (mt) cc_final: 0.7217 (mt) REVERT: C 31 GLU cc_start: 0.7086 (pt0) cc_final: 0.6704 (tt0) REVERT: C 42 TRP cc_start: 0.8285 (m100) cc_final: 0.7994 (m100) REVERT: C 104 TRP cc_start: 0.7378 (m100) cc_final: 0.6612 (m100) REVERT: C 108 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6615 (tm-30) REVERT: C 138 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7244 (tmtm) REVERT: C 156 LEU cc_start: 0.8221 (mt) cc_final: 0.8019 (mp) REVERT: C 209 CYS cc_start: 0.7628 (t) cc_final: 0.7276 (t) REVERT: C 254 THR cc_start: 0.7941 (t) cc_final: 0.7678 (m) REVERT: C 300 GLU cc_start: 0.6006 (tm-30) cc_final: 0.5513 (tm-30) REVERT: C 301 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7648 (ttm110) REVERT: C 335 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6666 (mm) REVERT: C 336 SER cc_start: 0.7632 (m) cc_final: 0.7379 (p) REVERT: C 362 LEU cc_start: 0.1611 (OUTLIER) cc_final: 0.1356 (mt) REVERT: D 5 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6559 (tm-30) REVERT: D 11 ILE cc_start: 0.8329 (mt) cc_final: 0.7936 (tt) REVERT: D 42 LEU cc_start: 0.7642 (mp) cc_final: 0.7381 (tp) REVERT: D 43 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6679 (m-10) REVERT: D 119 ASN cc_start: 0.7752 (t0) cc_final: 0.7414 (t0) REVERT: D 238 ASP cc_start: 0.7040 (m-30) cc_final: 0.6707 (m-30) REVERT: D 241 ILE cc_start: 0.7917 (mt) cc_final: 0.7641 (tt) REVERT: D 245 HIS cc_start: 0.7195 (t70) cc_final: 0.6808 (t70) REVERT: D 247 PHE cc_start: 0.6604 (t80) cc_final: 0.6323 (t80) REVERT: D 259 LYS cc_start: 0.8823 (mtmm) cc_final: 0.8312 (mttp) REVERT: D 267 ARG cc_start: 0.8515 (ttm110) cc_final: 0.7781 (ttm-80) REVERT: E 14 LYS cc_start: 0.8348 (mmmt) cc_final: 0.8147 (mmmt) REVERT: E 47 TYR cc_start: 0.7672 (t80) cc_final: 0.7455 (t80) REVERT: E 93 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8154 (mttm) REVERT: E 123 LYS cc_start: 0.8052 (mmmm) cc_final: 0.7735 (mmmm) REVERT: E 155 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8651 (mmtm) REVERT: F 91 MET cc_start: 0.8088 (mmm) cc_final: 0.7865 (mmm) REVERT: G 86 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.6861 (t80) REVERT: G 90 ASP cc_start: 0.7989 (t70) cc_final: 0.7279 (t70) REVERT: G 108 LYS cc_start: 0.8198 (mttp) cc_final: 0.7686 (tttp) REVERT: H 12 ASN cc_start: 0.7137 (p0) cc_final: 0.6881 (p0) REVERT: H 61 LYS cc_start: 0.8329 (mtmm) cc_final: 0.8080 (mtmm) REVERT: H 83 GLU cc_start: 0.7182 (pp20) cc_final: 0.6892 (pp20) REVERT: H 84 LYS cc_start: 0.8168 (mttm) cc_final: 0.7414 (mttm) REVERT: H 111 ASN cc_start: 0.8062 (m110) cc_final: 0.7739 (m-40) REVERT: H 121 GLN cc_start: 0.7999 (pp30) cc_final: 0.7694 (pp30) REVERT: H 154 ASP cc_start: 0.6401 (t70) cc_final: 0.6064 (t70) REVERT: H 241 GLU cc_start: 0.5798 (tm-30) cc_final: 0.5579 (tm-30) REVERT: H 305 MET cc_start: 0.6280 (ttp) cc_final: 0.5835 (tpp) REVERT: H 314 GLN cc_start: 0.7375 (tm-30) cc_final: 0.6784 (tm-30) REVERT: H 338 SER cc_start: 0.5392 (OUTLIER) cc_final: 0.4835 (t) REVERT: I 16 LEU cc_start: 0.7470 (tp) cc_final: 0.7034 (mt) REVERT: I 43 VAL cc_start: 0.7101 (p) cc_final: 0.6863 (m) REVERT: I 100 GLU cc_start: 0.7556 (tp30) cc_final: 0.7054 (tp30) REVERT: I 107 GLU cc_start: 0.6688 (pm20) cc_final: 0.6366 (pm20) REVERT: I 241 GLU cc_start: 0.7228 (tt0) cc_final: 0.6932 (tt0) REVERT: I 248 ILE cc_start: 0.7561 (mm) cc_final: 0.7178 (pt) REVERT: I 314 GLN cc_start: 0.6834 (tp-100) cc_final: 0.6499 (tp-100) REVERT: I 316 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7516 (mm-30) REVERT: I 353 GLN cc_start: 0.6908 (mt0) cc_final: 0.6560 (mp10) REVERT: N 72 GLU cc_start: 0.6842 (tp30) cc_final: 0.6518 (mp0) REVERT: N 119 MET cc_start: 0.6566 (ttp) cc_final: 0.6328 (ttp) REVERT: N 154 ASP cc_start: 0.7473 (t0) cc_final: 0.6946 (t0) REVERT: N 191 LYS cc_start: 0.7937 (ttpp) cc_final: 0.7406 (tppt) REVERT: N 238 LYS cc_start: 0.7696 (mmtm) cc_final: 0.7064 (mmtm) REVERT: N 244 ASP cc_start: 0.7670 (p0) cc_final: 0.7247 (p0) REVERT: N 279 TYR cc_start: 0.7363 (t80) cc_final: 0.6471 (t80) REVERT: N 282 ILE cc_start: 0.7584 (tt) cc_final: 0.7354 (pt) REVERT: N 350 SER cc_start: 0.8365 (m) cc_final: 0.8045 (p) REVERT: O 106 THR cc_start: 0.7360 (m) cc_final: 0.7086 (p) REVERT: O 216 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6137 (pp) REVERT: O 227 MET cc_start: 0.7763 (mmm) cc_final: 0.7067 (mmm) REVERT: O 282 ILE cc_start: 0.8512 (tt) cc_final: 0.8298 (tt) REVERT: O 313 MET cc_start: 0.6670 (mmm) cc_final: 0.6399 (tpp) REVERT: O 326 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6893 (mmmt) REVERT: O 335 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7782 (ptt-90) REVERT: P 47 MET cc_start: 0.4499 (mmt) cc_final: 0.3876 (mtt) REVERT: P 72 GLU cc_start: 0.6064 (mm-30) cc_final: 0.5843 (mm-30) REVERT: P 91 TYR cc_start: 0.8189 (m-80) cc_final: 0.7989 (m-80) REVERT: P 111 ASN cc_start: 0.7541 (m110) cc_final: 0.7226 (m-40) REVERT: P 134 VAL cc_start: 0.7594 (t) cc_final: 0.7230 (m) REVERT: P 161 HIS cc_start: 0.7315 (p90) cc_final: 0.6919 (p-80) REVERT: P 176 MET cc_start: 0.7094 (mtt) cc_final: 0.6575 (mmm) REVERT: P 195 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.6193 (pt0) REVERT: P 226 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7060 (mm-30) REVERT: P 275 HIS cc_start: 0.6941 (p-80) cc_final: 0.6312 (p-80) REVERT: P 335 ARG cc_start: 0.8489 (mtm180) cc_final: 0.8209 (mpp80) REVERT: Q 30 VAL cc_start: 0.7592 (t) cc_final: 0.7350 (p) REVERT: Q 149 THR cc_start: 0.8282 (p) cc_final: 0.8039 (p) REVERT: Q 191 LYS cc_start: 0.6969 (mmmm) cc_final: 0.6724 (mmtm) REVERT: Q 261 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8513 (mp) REVERT: Q 283 MET cc_start: 0.6947 (mmt) cc_final: 0.6723 (mmt) REVERT: Q 305 MET cc_start: 0.7411 (mmm) cc_final: 0.6689 (mmm) REVERT: Q 335 ARG cc_start: 0.7503 (mtm110) cc_final: 0.6689 (mtm180) REVERT: Q 360 GLN cc_start: 0.7399 (tp40) cc_final: 0.6965 (tp40) REVERT: R 57 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6955 (mm-30) REVERT: R 82 MET cc_start: 0.7581 (tpp) cc_final: 0.7361 (tpp) REVERT: R 121 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7523 (tm-30) REVERT: R 127 PHE cc_start: 0.6609 (m-80) cc_final: 0.6363 (m-80) REVERT: R 128 ASN cc_start: 0.8008 (m110) cc_final: 0.7741 (m110) REVERT: R 143 TYR cc_start: 0.7817 (m-80) cc_final: 0.7616 (m-80) REVERT: R 238 LYS cc_start: 0.8424 (tppt) cc_final: 0.8149 (mmtm) REVERT: S 16 LEU cc_start: 0.6992 (tt) cc_final: 0.6653 (mp) REVERT: S 82 MET cc_start: 0.7037 (tpt) cc_final: 0.6156 (tpt) REVERT: S 86 TRP cc_start: 0.7272 (OUTLIER) cc_final: 0.6687 (m-10) REVERT: S 120 THR cc_start: 0.7243 (m) cc_final: 0.7026 (t) REVERT: S 132 MET cc_start: 0.5453 (ppp) cc_final: 0.5110 (ppp) REVERT: S 142 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7526 (mp) REVERT: S 195 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6227 (pt0) REVERT: S 201 VAL cc_start: 0.7335 (OUTLIER) cc_final: 0.7123 (t) REVERT: S 253 GLU cc_start: 0.7668 (tp30) cc_final: 0.7244 (tp30) REVERT: S 283 MET cc_start: 0.7134 (tpp) cc_final: 0.6696 (mpp) REVERT: S 359 LYS cc_start: 0.6805 (OUTLIER) cc_final: 0.6543 (mttm) REVERT: g 1 TRP cc_start: 0.5716 (m100) cc_final: 0.5024 (m100) outliers start: 174 outliers final: 134 residues processed: 1325 average time/residue: 0.6183 time to fit residues: 1365.0003 Evaluate side-chains 1379 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1227 time to evaluate : 5.813 ------------------------------------------------------------------------------- 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 51 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 269 HIS Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain C residue 26 CYS Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 162 CYS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 283 MET Chi-restraints excluded: chain H residue 284 LYS Chi-restraints excluded: chain H residue 289 ILE Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 299 MET Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 360 GLN Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 31 PHE Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 325 MET Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 176 MET Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain N residue 291 LYS 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 351 THR Chi-restraints excluded: chain N residue 357 ILE Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 175 ILE Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 260 THR Chi-restraints excluded: chain O residue 294 TYR Chi-restraints excluded: chain O residue 299 MET Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 326 LYS Chi-restraints excluded: chain O residue 335 ARG Chi-restraints excluded: chain P residue 12 ASN Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 80 ASP 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 195 GLU Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 261 LEU Chi-restraints excluded: chain Q residue 326 LYS Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 339 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 300 SER Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 351 THR Chi-restraints excluded: chain R residue 361 GLU Chi-restraints excluded: chain S residue 75 ILE Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 278 THR Chi-restraints excluded: chain S residue 359 LYS Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain e residue 5 CYS Chi-restraints excluded: chain o residue 5 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 619 optimal weight: 3.9990 chunk 652 optimal weight: 8.9990 chunk 595 optimal weight: 1.9990 chunk 635 optimal weight: 10.0000 chunk 382 optimal weight: 1.9990 chunk 276 optimal weight: 7.9990 chunk 498 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 573 optimal weight: 0.9980 chunk 600 optimal weight: 0.0060 chunk 632 optimal weight: 0.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS C 33 HIS ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 231 HIS ** D 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 ASN I 12 ASN ** N 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 HIS ** S 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 51631 Z= 0.231 Angle : 0.677 13.572 70446 Z= 0.331 Chirality : 0.047 0.310 8177 Planarity : 0.004 0.053 9225 Dihedral : 8.683 146.791 8022 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.28 % Allowed : 25.11 % Favored : 70.62 % 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: -0.45 (0.10), residues: 7041 helix: 0.67 (0.10), residues: 2623 sheet: -0.35 (0.16), residues: 1075 loop : -1.02 (0.11), residues: 3343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 79 HIS 0.013 0.001 HIS D 254 PHE 0.031 0.002 PHE F 25 TYR 0.029 0.002 TYR S 279 ARG 0.012 0.000 ARG R 290 *********************** REFINEMENT MACRO_CYCLE 9 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 1417 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1238 time to evaluate : 5.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.6980 (mmm) cc_final: 0.6658 (mmt) REVERT: A 55 VAL cc_start: 0.7887 (t) cc_final: 0.7478 (p) REVERT: A 94 GLU cc_start: 0.7713 (pp20) cc_final: 0.7377 (pp20) REVERT: A 99 LYS cc_start: 0.7855 (mtpp) cc_final: 0.7448 (mtmm) REVERT: A 107 ASP cc_start: 0.7582 (t0) cc_final: 0.7235 (t0) REVERT: A 130 MET cc_start: 0.7912 (mmm) cc_final: 0.7187 (mpp) REVERT: A 135 ASN cc_start: 0.7769 (m110) cc_final: 0.7373 (m-40) REVERT: A 294 GLN cc_start: 0.7910 (tt0) cc_final: 0.7495 (tt0) REVERT: A 305 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7259 (mm-40) REVERT: A 371 HIS cc_start: 0.7281 (p-80) cc_final: 0.6857 (p-80) REVERT: A 406 SER cc_start: 0.7981 (p) cc_final: 0.7704 (m) REVERT: B 7 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8123 (ptmt) REVERT: B 46 LYS cc_start: 0.7832 (tptp) cc_final: 0.7462 (tptp) REVERT: B 57 VAL cc_start: 0.8177 (OUTLIER) cc_final: 0.7951 (p) REVERT: B 86 LYS cc_start: 0.8389 (ttpp) cc_final: 0.8094 (ttpp) REVERT: B 105 CYS cc_start: 0.7857 (m) cc_final: 0.7066 (m) REVERT: B 141 GLN cc_start: 0.7517 (mp10) cc_final: 0.7266 (mp10) REVERT: B 145 THR cc_start: 0.6900 (OUTLIER) cc_final: 0.6680 (p) REVERT: B 146 LEU cc_start: 0.7565 (mp) cc_final: 0.6971 (mp) REVERT: B 181 ARG cc_start: 0.7295 (ttp80) cc_final: 0.6839 (ttt-90) REVERT: B 195 LYS cc_start: 0.6751 (tppt) cc_final: 0.6451 (tppt) REVERT: B 226 ASN cc_start: 0.8503 (t0) cc_final: 0.8277 (t0) REVERT: B 263 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6348 (tp30) REVERT: C 13 CYS cc_start: 0.6909 (t) cc_final: 0.6599 (t) REVERT: C 31 GLU cc_start: 0.7034 (pt0) cc_final: 0.6642 (tt0) REVERT: C 42 TRP cc_start: 0.8297 (m100) cc_final: 0.7978 (m100) REVERT: C 104 TRP cc_start: 0.7382 (m100) cc_final: 0.6438 (m100) REVERT: C 108 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6616 (tp30) REVERT: C 138 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7279 (tmtm) REVERT: C 209 CYS cc_start: 0.7674 (t) cc_final: 0.7324 (t) REVERT: C 254 THR cc_start: 0.7999 (t) cc_final: 0.7788 (m) REVERT: C 300 GLU cc_start: 0.6091 (tm-30) cc_final: 0.5580 (tm-30) REVERT: C 301 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.6966 (ttm110) REVERT: C 335 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6683 (mm) REVERT: C 336 SER cc_start: 0.7645 (m) cc_final: 0.7384 (p) REVERT: D 5 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6586 (tm-30) REVERT: D 11 ILE cc_start: 0.8286 (mt) cc_final: 0.7954 (tt) REVERT: D 42 LEU cc_start: 0.7642 (mp) cc_final: 0.7368 (tp) REVERT: D 43 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6689 (m-10) REVERT: D 119 ASN cc_start: 0.7778 (t0) cc_final: 0.7426 (t0) REVERT: D 238 ASP cc_start: 0.7065 (m-30) cc_final: 0.6715 (m-30) REVERT: D 241 ILE cc_start: 0.7874 (mt) cc_final: 0.7623 (tt) REVERT: D 245 HIS cc_start: 0.7179 (t70) cc_final: 0.6801 (t70) REVERT: D 247 PHE cc_start: 0.6621 (t80) cc_final: 0.6324 (t80) REVERT: D 259 LYS cc_start: 0.8796 (mtmm) cc_final: 0.8321 (mttp) REVERT: E 14 LYS cc_start: 0.8351 (mmmt) cc_final: 0.8149 (mmmt) REVERT: E 47 TYR cc_start: 0.7684 (t80) cc_final: 0.7473 (t80) REVERT: E 93 LYS cc_start: 0.8509 (mmmt) cc_final: 0.8165 (mttm) REVERT: E 123 LYS cc_start: 0.8033 (mmmm) cc_final: 0.7739 (mmmm) REVERT: E 155 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8643 (mmtm) REVERT: F 96 MET cc_start: 0.6251 (tpt) cc_final: 0.5890 (tpt) REVERT: G 86 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.6883 (t80) REVERT: G 90 ASP cc_start: 0.7991 (t70) cc_final: 0.7338 (t70) REVERT: G 108 LYS cc_start: 0.8168 (mttp) cc_final: 0.7585 (tttp) REVERT: G 131 LYS cc_start: 0.8355 (mmtm) cc_final: 0.8074 (mmmm) REVERT: H 12 ASN cc_start: 0.7136 (p0) cc_final: 0.6881 (p0) REVERT: H 16 LEU cc_start: 0.7022 (mp) cc_final: 0.6726 (mt) REVERT: H 61 LYS cc_start: 0.8367 (mtmm) cc_final: 0.8108 (mtmm) REVERT: H 83 GLU cc_start: 0.7179 (pp20) cc_final: 0.6896 (pp20) REVERT: H 84 LYS cc_start: 0.8166 (mttm) cc_final: 0.7406 (mttm) REVERT: H 111 ASN cc_start: 0.7975 (m110) cc_final: 0.7748 (m-40) REVERT: H 121 GLN cc_start: 0.8006 (pp30) cc_final: 0.7682 (pp30) REVERT: H 154 ASP cc_start: 0.6354 (t70) cc_final: 0.6009 (t70) REVERT: H 241 GLU cc_start: 0.5818 (tm-30) cc_final: 0.5601 (tm-30) REVERT: H 305 MET cc_start: 0.6307 (ttp) cc_final: 0.5873 (tpp) REVERT: H 314 GLN cc_start: 0.7336 (tm-30) cc_final: 0.6818 (tm-30) REVERT: H 338 SER cc_start: 0.5399 (OUTLIER) cc_final: 0.4839 (t) REVERT: I 16 LEU cc_start: 0.7493 (tp) cc_final: 0.7083 (mt) REVERT: I 43 VAL cc_start: 0.7146 (p) cc_final: 0.6909 (m) REVERT: I 100 GLU cc_start: 0.7545 (tp30) cc_final: 0.7073 (tp30) REVERT: I 107 GLU cc_start: 0.6734 (pm20) cc_final: 0.6384 (pm20) REVERT: I 121 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8070 (tm-30) REVERT: I 241 GLU cc_start: 0.7253 (tt0) cc_final: 0.6951 (tt0) REVERT: I 248 ILE cc_start: 0.7606 (mm) cc_final: 0.7177 (pt) REVERT: I 314 GLN cc_start: 0.6813 (tp-100) cc_final: 0.6499 (tp-100) REVERT: I 353 GLN cc_start: 0.7180 (mt0) cc_final: 0.6743 (mp10) REVERT: N 72 GLU cc_start: 0.6881 (tp30) cc_final: 0.6547 (mp0) REVERT: N 154 ASP cc_start: 0.7453 (t0) cc_final: 0.6949 (t0) REVERT: N 191 LYS cc_start: 0.7965 (ttpp) cc_final: 0.7421 (tppt) REVERT: N 238 LYS cc_start: 0.7732 (mmtm) cc_final: 0.7100 (mmtm) REVERT: N 244 ASP cc_start: 0.7665 (p0) cc_final: 0.7239 (p0) REVERT: N 279 TYR cc_start: 0.7403 (t80) cc_final: 0.6548 (t80) REVERT: N 282 ILE cc_start: 0.7614 (tt) cc_final: 0.7386 (pt) REVERT: N 350 SER cc_start: 0.8379 (m) cc_final: 0.8043 (p) REVERT: O 106 THR cc_start: 0.7347 (m) cc_final: 0.7065 (p) REVERT: O 216 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6119 (pp) REVERT: O 224 GLU cc_start: 0.7875 (mp0) cc_final: 0.7600 (tp30) REVERT: O 282 ILE cc_start: 0.8532 (tt) cc_final: 0.8306 (tt) REVERT: O 313 MET cc_start: 0.6670 (mmm) cc_final: 0.6277 (tpp) REVERT: O 326 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6888 (mmmt) REVERT: P 47 MET cc_start: 0.4513 (mmt) cc_final: 0.3953 (mtt) REVERT: P 111 ASN cc_start: 0.7552 (m110) cc_final: 0.7246 (m-40) REVERT: P 123 MET cc_start: 0.7395 (mmm) cc_final: 0.7010 (mmm) REVERT: P 161 HIS cc_start: 0.7347 (p90) cc_final: 0.6931 (p-80) REVERT: P 176 MET cc_start: 0.7127 (mtt) cc_final: 0.6622 (mmm) REVERT: P 195 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6344 (pt0) REVERT: P 226 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7080 (mm-30) REVERT: P 335 ARG cc_start: 0.8598 (mtm180) cc_final: 0.8243 (mpp80) REVERT: Q 30 VAL cc_start: 0.7558 (t) cc_final: 0.7291 (p) REVERT: Q 107 GLU cc_start: 0.7403 (pt0) cc_final: 0.7158 (pt0) REVERT: Q 149 THR cc_start: 0.8257 (p) cc_final: 0.8019 (p) REVERT: Q 191 LYS cc_start: 0.6895 (mmmm) cc_final: 0.6655 (mmtm) REVERT: Q 305 MET cc_start: 0.7471 (mmm) cc_final: 0.6803 (mmm) REVERT: Q 335 ARG cc_start: 0.7483 (mtm110) cc_final: 0.6635 (mtm180) REVERT: Q 360 GLN cc_start: 0.7404 (tp40) cc_final: 0.6992 (tp40) REVERT: R 57 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7034 (mm-30) REVERT: R 82 MET cc_start: 0.7583 (tpp) cc_final: 0.7375 (tpp) REVERT: R 85 ILE cc_start: 0.8322 (tt) cc_final: 0.7977 (tp) REVERT: R 121 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7472 (tm-30) REVERT: R 128 ASN cc_start: 0.8021 (m110) cc_final: 0.7758 (m110) REVERT: R 143 TYR cc_start: 0.7857 (m-80) cc_final: 0.7620 (m-80) REVERT: R 238 LYS cc_start: 0.8442 (tppt) cc_final: 0.8180 (mmtm) REVERT: S 16 LEU cc_start: 0.6988 (tt) cc_final: 0.6664 (mp) REVERT: S 82 MET cc_start: 0.7062 (tpt) cc_final: 0.6229 (tpt) REVERT: S 86 TRP cc_start: 0.7294 (OUTLIER) cc_final: 0.6547 (m-10) REVERT: S 120 THR cc_start: 0.7210 (m) cc_final: 0.6983 (t) REVERT: S 132 MET cc_start: 0.5425 (ppp) cc_final: 0.5156 (ppp) REVERT: S 154 ASP cc_start: 0.7235 (t0) cc_final: 0.6939 (t0) REVERT: S 195 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6224 (pt0) REVERT: S 201 VAL cc_start: 0.7418 (OUTLIER) cc_final: 0.7147 (t) REVERT: S 253 GLU cc_start: 0.7683 (tp30) cc_final: 0.7241 (tp30) REVERT: S 283 MET cc_start: 0.7158 (tpp) cc_final: 0.6696 (mpp) REVERT: g 1 TRP cc_start: 0.5666 (m100) cc_final: 0.5029 (m100) outliers start: 179 outliers final: 147 residues processed: 1317 average time/residue: 0.6124 time to fit residues: 1341.5289 Evaluate side-chains 1395 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1235 time to evaluate : 5.185 ------------------------------------------------------------------------------- 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 51 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain C residue 26 CYS Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 162 CYS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 283 MET Chi-restraints excluded: chain H residue 284 LYS Chi-restraints excluded: chain H residue 289 ILE Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 360 GLN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 31 PHE Chi-restraints excluded: chain I residue 173 HIS Chi-restraints excluded: chain I residue 213 LYS Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 325 MET Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 176 MET Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain N residue 291 LYS 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 351 THR Chi-restraints excluded: chain N residue 357 ILE Chi-restraints excluded: chain O residue 12 ASN Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 175 ILE Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 260 THR Chi-restraints excluded: chain O residue 294 TYR Chi-restraints excluded: chain O residue 299 MET Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 326 LYS Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 80 ASP 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 358 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 214 GLU Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain Q residue 326 LYS Chi-restraints excluded: chain Q residue 329 ILE Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 339 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 351 THR Chi-restraints excluded: chain R residue 361 GLU Chi-restraints excluded: chain S residue 75 ILE Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 278 THR Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain e residue 5 CYS Chi-restraints excluded: chain h residue 5 CYS Chi-restraints excluded: chain o residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 416 optimal weight: 0.9980 chunk 671 optimal weight: 30.0000 chunk 409 optimal weight: 10.0000 chunk 318 optimal weight: 4.9990 chunk 466 optimal weight: 1.9990 chunk 704 optimal weight: 10.0000 chunk 648 optimal weight: 10.0000 chunk 560 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 433 optimal weight: 3.9990 chunk 343 optimal weight: 40.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN C 33 HIS ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 231 HIS D 254 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 115 ASN ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 137 GLN Q 371 HIS ** R 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 HIS ** S 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.249 51631 Z= 0.596 Angle : 0.930 14.621 70446 Z= 0.479 Chirality : 0.057 0.364 8177 Planarity : 0.006 0.079 9225 Dihedral : 9.825 150.057 8022 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.66 % Favored : 91.22 % Rotamer: Outliers : 4.71 % Allowed : 25.16 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.48 (0.10), residues: 7041 helix: -0.34 (0.10), residues: 2687 sheet: -0.76 (0.16), residues: 1078 loop : -1.56 (0.11), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.004 TRP n 1 HIS 0.025 0.003 HIS D 231 PHE 0.043 0.003 PHE A 331 TYR 0.040 0.004 TYR O 53 ARG 0.025 0.001 ARG D 230 ********************** REFINEMENT MACRO_CYCLE 10 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 1470 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1273 time to evaluate : 5.896 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: A 52 MET cc_start: 0.7078 (mmm) cc_final: 0.6799 (mmt) REVERT: A 94 GLU cc_start: 0.7807 (pp20) cc_final: 0.7481 (pp20) REVERT: A 99 LYS cc_start: 0.7859 (mtpp) cc_final: 0.7518 (mtmm) REVERT: A 107 ASP cc_start: 0.7836 (t0) cc_final: 0.7490 (t0) REVERT: A 130 MET cc_start: 0.7959 (mmm) cc_final: 0.7352 (mmm) REVERT: A 135 ASN cc_start: 0.7673 (m110) cc_final: 0.7440 (m-40) REVERT: A 305 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7528 (mm-40) REVERT: A 371 HIS cc_start: 0.7361 (p-80) cc_final: 0.6775 (p-80) REVERT: A 372 MET cc_start: 0.7160 (ttm) cc_final: 0.6351 (tmm) REVERT: A 406 SER cc_start: 0.8116 (p) cc_final: 0.7860 (m) REVERT: B 7 LYS cc_start: 0.8192 (ttmt) cc_final: 0.7971 (ptmt) REVERT: B 46 LYS cc_start: 0.7857 (tptp) cc_final: 0.7502 (tptp) REVERT: B 57 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7968 (p) REVERT: B 74 MET cc_start: 0.7022 (mmp) cc_final: 0.6573 (mmm) REVERT: B 86 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8162 (ttpp) REVERT: B 105 CYS cc_start: 0.7957 (m) cc_final: 0.7286 (m) REVERT: B 146 LEU cc_start: 0.7982 (mp) cc_final: 0.7679 (mp) REVERT: B 181 ARG cc_start: 0.7228 (ttp80) cc_final: 0.6881 (ttt-90) REVERT: B 226 ASN cc_start: 0.8620 (t0) cc_final: 0.8415 (t0) REVERT: B 263 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6510 (tp30) REVERT: B 274 GLU cc_start: 0.7803 (tp30) cc_final: 0.7485 (tp30) REVERT: B 320 GLU cc_start: 0.6967 (tp30) cc_final: 0.6681 (tp30) REVERT: C 13 CYS cc_start: 0.6991 (t) cc_final: 0.6666 (t) REVERT: C 31 GLU cc_start: 0.7146 (pt0) cc_final: 0.6772 (tt0) REVERT: C 42 TRP cc_start: 0.8439 (m100) cc_final: 0.8209 (m100) REVERT: C 90 LEU cc_start: 0.8238 (mt) cc_final: 0.7947 (mt) REVERT: C 104 TRP cc_start: 0.7533 (m100) cc_final: 0.6791 (m100) REVERT: C 108 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6836 (tm-30) REVERT: C 138 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7324 (tmtm) REVERT: C 209 CYS cc_start: 0.7747 (t) cc_final: 0.7499 (t) REVERT: C 300 GLU cc_start: 0.6506 (tm-30) cc_final: 0.5939 (tm-30) REVERT: C 301 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7778 (ttm110) REVERT: C 335 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6808 (mm) REVERT: D 5 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6671 (tm-30) REVERT: D 43 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.6747 (m-10) REVERT: D 119 ASN cc_start: 0.7750 (t0) cc_final: 0.7406 (t0) REVERT: D 241 ILE cc_start: 0.8066 (mt) cc_final: 0.7787 (tt) REVERT: D 247 PHE cc_start: 0.7016 (t80) cc_final: 0.6606 (t80) REVERT: D 259 LYS cc_start: 0.8701 (mtmm) cc_final: 0.8309 (mttp) REVERT: E 14 LYS cc_start: 0.8368 (mmmt) cc_final: 0.8074 (mmmt) REVERT: E 39 THR cc_start: 0.7824 (m) cc_final: 0.7599 (p) REVERT: E 93 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8192 (mttm) REVERT: E 155 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8660 (mmtm) REVERT: F 1 MET cc_start: 0.7085 (mpp) cc_final: 0.6884 (mpp) REVERT: G 86 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.6600 (t80) REVERT: G 90 ASP cc_start: 0.8136 (t70) cc_final: 0.7501 (t70) REVERT: G 108 LYS cc_start: 0.8225 (mttp) cc_final: 0.7629 (tttp) REVERT: H 14 SER cc_start: 0.4514 (m) cc_final: 0.4174 (p) REVERT: H 61 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8174 (mtmm) REVERT: H 83 GLU cc_start: 0.7214 (pp20) cc_final: 0.6927 (pp20) REVERT: H 84 LYS cc_start: 0.8290 (mttm) cc_final: 0.7421 (mttm) REVERT: H 88 HIS cc_start: 0.7502 (t-90) cc_final: 0.7298 (t70) REVERT: H 121 GLN cc_start: 0.7961 (pp30) cc_final: 0.7601 (pp30) REVERT: H 154 ASP cc_start: 0.6592 (t70) cc_final: 0.6282 (t70) REVERT: H 305 MET cc_start: 0.6371 (ttp) cc_final: 0.5910 (ttp) REVERT: H 314 GLN cc_start: 0.7642 (tm-30) cc_final: 0.7347 (tm-30) REVERT: H 338 SER cc_start: 0.5587 (OUTLIER) cc_final: 0.5235 (t) REVERT: I 43 VAL cc_start: 0.7528 (p) cc_final: 0.7241 (m) REVERT: I 92 ASN cc_start: 0.8438 (m110) cc_final: 0.8131 (m-40) REVERT: I 100 GLU cc_start: 0.7579 (tp30) cc_final: 0.7112 (tp30) REVERT: I 107 GLU cc_start: 0.6777 (pm20) cc_final: 0.6568 (pm20) REVERT: I 188 TYR cc_start: 0.7780 (t80) cc_final: 0.7470 (t80) REVERT: I 241 GLU cc_start: 0.7309 (tt0) cc_final: 0.7025 (tt0) REVERT: I 248 ILE cc_start: 0.7647 (mm) cc_final: 0.7105 (pt) REVERT: I 259 GLU cc_start: 0.7414 (tp30) cc_final: 0.6770 (tp30) REVERT: I 314 GLN cc_start: 0.7278 (tp-100) cc_final: 0.6912 (tp-100) REVERT: I 316 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7532 (mm-30) REVERT: N 82 MET cc_start: 0.4921 (tpt) cc_final: 0.4683 (tpp) REVERT: N 154 ASP cc_start: 0.7492 (t0) cc_final: 0.7020 (t0) REVERT: N 223 PHE cc_start: 0.6212 (t80) cc_final: 0.5620 (m-80) REVERT: N 238 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7076 (mmtm) REVERT: N 244 ASP cc_start: 0.7499 (p0) cc_final: 0.7110 (p0) REVERT: N 279 TYR cc_start: 0.7585 (t80) cc_final: 0.6912 (t80) REVERT: N 282 ILE cc_start: 0.7681 (tt) cc_final: 0.7430 (pt) REVERT: N 350 SER cc_start: 0.8333 (m) cc_final: 0.7988 (p) REVERT: O 12 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7394 (m-40) REVERT: O 106 THR cc_start: 0.7518 (m) cc_final: 0.7158 (p) REVERT: O 213 LYS cc_start: 0.7002 (ttmm) cc_final: 0.6660 (ttpt) REVERT: O 216 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6692 (pp) REVERT: O 224 GLU cc_start: 0.7911 (mp0) cc_final: 0.7661 (tp30) REVERT: O 227 MET cc_start: 0.7657 (mmm) cc_final: 0.7172 (mmm) REVERT: O 282 ILE cc_start: 0.8501 (tt) cc_final: 0.8296 (tt) REVERT: O 289 ILE cc_start: 0.8278 (pt) cc_final: 0.7940 (mt) REVERT: P 47 MET cc_start: 0.4598 (mmt) cc_final: 0.4042 (mtt) REVERT: P 76 ILE cc_start: 0.7903 (mm) cc_final: 0.7560 (mt) REVERT: P 111 ASN cc_start: 0.7477 (m110) cc_final: 0.7153 (m-40) REVERT: P 113 LYS cc_start: 0.7827 (mmtt) cc_final: 0.7406 (mmtt) REVERT: P 176 MET cc_start: 0.7011 (mtt) cc_final: 0.6580 (mmm) REVERT: P 195 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6371 (pt0) REVERT: P 226 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7160 (mm-30) REVERT: P 335 ARG cc_start: 0.8632 (mtm180) cc_final: 0.8159 (mtt180) REVERT: Q 141 SER cc_start: 0.8604 (m) cc_final: 0.8123 (p) REVERT: Q 149 THR cc_start: 0.8333 (p) cc_final: 0.8101 (p) REVERT: Q 335 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7238 (mtm180) REVERT: Q 360 GLN cc_start: 0.7467 (tp40) cc_final: 0.6901 (tp40) REVERT: R 57 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7284 (mm-30) REVERT: R 85 ILE cc_start: 0.8456 (tt) cc_final: 0.8130 (tp) REVERT: R 95 ARG cc_start: 0.6841 (mtm-85) cc_final: 0.6609 (mtm-85) REVERT: R 128 ASN cc_start: 0.8195 (m110) cc_final: 0.7910 (m-40) REVERT: R 139 VAL cc_start: 0.8409 (m) cc_final: 0.8014 (p) REVERT: R 143 TYR cc_start: 0.8074 (m-80) cc_final: 0.7827 (m-80) REVERT: R 177 ARG cc_start: 0.7835 (ttt-90) cc_final: 0.7591 (ttt180) REVERT: R 207 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7295 (mm-30) REVERT: R 235 SER cc_start: 0.8474 (p) cc_final: 0.8047 (t) REVERT: R 238 LYS cc_start: 0.8565 (tppt) cc_final: 0.8204 (mmtm) REVERT: S 82 MET cc_start: 0.7289 (tpt) cc_final: 0.6380 (tpt) REVERT: S 86 TRP cc_start: 0.7440 (OUTLIER) cc_final: 0.6527 (m-10) REVERT: S 154 ASP cc_start: 0.7360 (t0) cc_final: 0.7156 (t0) REVERT: S 195 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6460 (pt0) REVERT: S 201 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7449 (t) REVERT: S 325 MET cc_start: 0.6909 (pmm) cc_final: 0.5312 (mmt) REVERT: g 1 TRP cc_start: 0.6160 (m100) cc_final: 0.5539 (m100) outliers start: 197 outliers final: 154 residues processed: 1355 average time/residue: 0.6077 time to fit residues: 1380.2982 Evaluate side-chains 1405 residues out of total 6097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1239 time to evaluate : 5.132 ------------------------------------------------------------------------------- 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 21 TYR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 26 CYS Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 162 CYS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 283 MET Chi-restraints excluded: chain H residue 284 LYS Chi-restraints excluded: chain H residue 289 ILE Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 31 PHE Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 213 LYS Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 325 MET Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain N residue 225 ASN Chi-restraints excluded: chain N residue 291 LYS 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 351 THR Chi-restraints excluded: chain O residue 12 ASN Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 175 ILE Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 260 THR Chi-restraints excluded: chain O residue 294 TYR Chi-restraints excluded: chain O residue 299 MET Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 80 ASP 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 190 MET Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 305 MET Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 373 LYS Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 214 GLU Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain Q residue 326 LYS Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 339 VAL Chi-restraints excluded: chain Q residue 341 ILE Chi-restraints excluded: chain Q residue 351 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 218 TYR Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 361 GLU Chi-restraints excluded: chain R residue 364 GLU Chi-restraints excluded: chain S residue 75 ILE Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 278 THR Chi-restraints excluded: chain e residue 5 CYS Chi-restraints excluded: chain h residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 445 optimal weight: 0.7980 chunk 597 optimal weight: 0.8980 chunk 171 optimal weight: 0.0770 chunk 517 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 561 optimal weight: 0.0010 chunk 235 optimal weight: 1.9990 chunk 576 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 overall best weight: 0.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 252 ASN ** O 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 HIS ** R 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 HIS ** S 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.168418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.143902 restraints weight = 95577.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147428 restraints weight = 56060.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.149770 restraints weight = 36191.882| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.292 51631 Z= 0.474 Angle : 0.986 59.199 70446 Z= 0.525 Chirality : 0.054 0.656 8177 Planarity : 0.006 0.153 9225 Dihedral : 9.800 149.955 8022 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.59 % Favored : 91.38 % Rotamer: Outliers : 4.63 % Allowed : 25.97 % Favored : 69.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.51 (0.10), residues: 7041 helix: -0.35 (0.10), residues: 2681 sheet: -0.80 (0.16), residues: 1078 loop : -1.57 (0.11), residues: 3282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.115 0.004 TRP A 153 HIS 0.191 0.003 HIS D 231 PHE 0.039 0.003 PHE C 252 TYR 0.040 0.003 TYR O 53 ARG 0.010 0.001 ARG D 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18266.97 seconds wall clock time: 325 minutes 26.57 seconds (19526.57 seconds total)