Starting phenix.real_space_refine on Fri Aug 9 06:38:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0l_31400/08_2024/7f0l_31400.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0l_31400/08_2024/7f0l_31400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0l_31400/08_2024/7f0l_31400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0l_31400/08_2024/7f0l_31400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0l_31400/08_2024/7f0l_31400.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0l_31400/08_2024/7f0l_31400.cif" } resolution = 2.94 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= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 21 5.49 5 Mg 32 5.21 5 S 88 5.16 5 C 16545 2.51 5 N 3101 2.21 5 O 3670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 23458 Number of models: 1 Model: "" Number of chains: 66 Chain: "L" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2233 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2437 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 293} Chain: "H" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1864 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 222} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 386 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "I" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 453 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 454 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "V" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "1" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "5" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "6" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 332 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "7" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 415 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "8" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "X" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 405 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "U" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 369 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "L" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 482 Unusual residues: {'BCL': 3, 'BPH': 1, 'LDA': 2, 'PGV': 3, 'U10': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 2, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 49 Chain: "M" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 497 Unusual residues: {' FE': 1, 'BCL': 1, 'BPH': 1, 'CDL': 1, 'LDA': 1, 'LMT': 3, 'PGV': 2, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PGV:plan-3': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 284 Unusual residues: {'CDL': 2, 'LMT': 2, 'PGV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 158 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 193 Unusual residues: {'BCL': 1, 'LMT': 2, 'SPO': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 184 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'BCL': 1, 'LMT': 2, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 205 Unusual residues: {'BCL': 1, 'LMT': 2, 'SPO': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 169 Unusual residues: {'BCL': 1, 'CDL': 1, 'LDA': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "4" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "5" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 183 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "6" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 141 Unusual residues: {'LDA': 2, 'LMT': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "U" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 12.81, per 1000 atoms: 0.55 Number of scatterers: 23458 At special positions: 0 Unit cell: (132.374, 114.87, 137.844, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 88 16.00 P 21 15.00 Mg 32 11.99 O 3670 8.00 N 3101 7.00 C 16545 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.34 Conformation dependent library (CDL) restraints added in 3.3 seconds 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 8 sheets defined 72.8% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'L' and resid 6 through 10 removed outlier: 3.610A pdb=" N ARG L 10 " --> pdb=" O ARG L 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.575A pdb=" N VAL L 54 " --> pdb=" O ALA L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 74 removed outlier: 3.589A pdb=" N GLY L 74 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 112 removed outlier: 3.523A pdb=" N GLU L 106 " --> pdb=" O LEU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.628A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 removed outlier: 3.810A pdb=" N TYR L 144 " --> pdb=" O ALA L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 164 removed outlier: 3.640A pdb=" N ASP L 155 " --> pdb=" O TRP L 151 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 169 removed outlier: 5.929A pdb=" N HIS L 168 " --> pdb=" O GLY L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 221 removed outlier: 3.549A pdb=" N PHE L 216 " --> pdb=" O GLU L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 250 removed outlier: 3.899A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET L 248 " --> pdb=" O SER L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 262 No H-bonds generated for 'chain 'L' and resid 260 through 262' Processing helix chain 'L' and resid 263 through 268 removed outlier: 3.670A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 41 Processing helix chain 'M' and resid 53 through 78 Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 112 through 140 removed outlier: 3.731A pdb=" N LEU M 116 " --> pdb=" O GLY M 112 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA M 137 " --> pdb=" O THR M 133 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 162 removed outlier: 3.612A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU M 156 " --> pdb=" O SER M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 Processing helix chain 'M' and resid 180 through 193 Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 257 removed outlier: 3.623A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 286 removed outlier: 3.861A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE M 282 " --> pdb=" O LEU M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 300 Processing helix chain 'H' and resid 12 through 34 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 209 through 216 removed outlier: 3.510A pdb=" N LEU H 212 " --> pdb=" O SER H 209 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE H 213 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 239 Processing helix chain 'H' and resid 239 through 244 Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 12 through 38 removed outlier: 4.280A pdb=" N VAL A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 45 removed outlier: 3.584A pdb=" N GLN B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 10 removed outlier: 3.747A pdb=" N LYS D 6 " --> pdb=" O LYS D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 38 removed outlier: 3.565A pdb=" N VAL D 18 " --> pdb=" O ARG D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 41 No H-bonds generated for 'chain 'D' and resid 39 through 41' Processing helix chain 'D' and resid 42 through 51 removed outlier: 3.514A pdb=" N SER D 47 " --> pdb=" O TRP D 43 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 45 Processing helix chain 'F' and resid 3 through 10 removed outlier: 3.658A pdb=" N LYS F 6 " --> pdb=" O LYS F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 38 Processing helix chain 'F' and resid 39 through 41 No H-bonds generated for 'chain 'F' and resid 39 through 41' Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'G' and resid 12 through 45 Processing helix chain 'I' and resid 1 through 10 removed outlier: 3.967A pdb=" N TYR I 5 " --> pdb=" O SER I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 38 Processing helix chain 'I' and resid 42 through 52 Processing helix chain 'J' and resid 12 through 45 Processing helix chain 'K' and resid 3 through 10 removed outlier: 3.864A pdb=" N LYS K 6 " --> pdb=" O LYS K 3 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP K 8 " --> pdb=" O TYR K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 37 removed outlier: 3.584A pdb=" N VAL K 18 " --> pdb=" O ARG K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 51 Processing helix chain 'N' and resid 12 through 45 Processing helix chain 'O' and resid 3 through 10 removed outlier: 3.685A pdb=" N TRP O 8 " --> pdb=" O TYR O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 38 Processing helix chain 'O' and resid 42 through 52 removed outlier: 3.633A pdb=" N SER O 47 " --> pdb=" O TRP O 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 12 through 38 Processing helix chain 'Q' and resid 42 through 52 removed outlier: 3.509A pdb=" N ALA Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 45 removed outlier: 3.602A pdb=" N VAL R 22 " --> pdb=" O GLU R 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 10 Processing helix chain 'S' and resid 12 through 38 removed outlier: 3.837A pdb=" N VAL S 18 " --> pdb=" O ARG S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 51 Processing helix chain 'T' and resid 12 through 45 Processing helix chain 'V' and resid 2 through 10 removed outlier: 4.048A pdb=" N TYR V 5 " --> pdb=" O SER V 2 " (cutoff:3.500A) Processing helix chain 'V' and resid 12 through 38 Processing helix chain 'V' and resid 42 through 52 Processing helix chain 'W' and resid 12 through 45 removed outlier: 3.502A pdb=" N VAL W 22 " --> pdb=" O GLU W 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 8 removed outlier: 3.802A pdb=" N TRP Y 8 " --> pdb=" O TYR Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 38 Processing helix chain 'Y' and resid 42 through 52 Processing helix chain 'Z' and resid 12 through 45 Processing helix chain '1' and resid 3 through 10 removed outlier: 3.605A pdb=" N LYS 1 6 " --> pdb=" O LYS 1 3 " (cutoff:3.500A) Processing helix chain '1' and resid 12 through 38 Processing helix chain '1' and resid 42 through 51 removed outlier: 3.543A pdb=" N ALA 1 48 " --> pdb=" O LEU 1 44 " (cutoff:3.500A) Processing helix chain '2' and resid 12 through 45 Processing helix chain '3' and resid 3 through 5 No H-bonds generated for 'chain '3' and resid 3 through 5' Processing helix chain '3' and resid 6 through 11 Processing helix chain '3' and resid 12 through 38 Processing helix chain '3' and resid 42 through 52 Processing helix chain '4' and resid 12 through 45 Processing helix chain '5' and resid 3 through 10 removed outlier: 3.729A pdb=" N LYS 5 6 " --> pdb=" O LYS 5 3 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE 5 10 " --> pdb=" O ILE 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 38 Processing helix chain '5' and resid 42 through 51 Processing helix chain '6' and resid 12 through 45 Processing helix chain '7' and resid 6 through 11 Processing helix chain '7' and resid 12 through 38 removed outlier: 3.550A pdb=" N PHE 7 17 " --> pdb=" O PRO 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 51 Processing helix chain '8' and resid 12 through 45 Processing helix chain 'X' and resid 18 through 54 Processing helix chain 'U' and resid 5 through 30 Processing helix chain 'U' and resid 31 through 48 removed outlier: 3.709A pdb=" N GLY U 35 " --> pdb=" O HIS U 31 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA U 48 " --> pdb=" O ALA U 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.806A pdb=" N PHE L 24 " --> pdb=" O VAL L 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.829A pdb=" N GLN M 11 " --> pdb=" O SER H 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 93 through 94 Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 7 removed outlier: 4.002A pdb=" N PHE H 7 " --> pdb=" O PHE H 10 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 62 through 65 Processing sheet with id=AA6, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA7, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.822A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL H 169 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA H 176 " --> pdb=" O VAL H 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.357A pdb=" N VAL H 153 " --> pdb=" O ALA H 161 " (cutoff:3.500A) 1271 hydrogen bonds defined for protein. 3600 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: 6.46 Time building geometry restraints manager: 10.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 6887 1.37 - 1.54: 17020 1.54 - 1.71: 113 1.71 - 1.88: 171 1.88 - 2.05: 128 Bond restraints: 24319 Sorted by residual: bond pdb=" CB7 CDL Y 102 " pdb=" OB8 CDL Y 102 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CA7 CDL H 304 " pdb=" OA8 CDL H 304 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CA7 CDL H 305 " pdb=" OA8 CDL H 305 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CB7 CDL H 304 " pdb=" OB8 CDL H 304 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.17e+02 bond pdb=" CA7 CDL Y 102 " pdb=" OA8 CDL Y 102 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.16e+02 ... (remaining 24314 not shown) Histogram of bond angle deviations from ideal: 83.21 - 102.39: 434 102.39 - 121.58: 27585 121.58 - 140.76: 5122 140.76 - 159.95: 36 159.95 - 179.13: 62 Bond angle restraints: 33239 Sorted by residual: angle pdb=" C51 CDL M 811 " pdb=" CB5 CDL M 811 " pdb=" OB6 CDL M 811 " ideal model delta sigma weight residual 111.33 122.29 -10.96 1.32e+00 5.72e-01 6.87e+01 angle pdb=" C1D BCL L 301 " pdb=" C2D BCL L 301 " pdb=" CMD BCL L 301 " ideal model delta sigma weight residual 125.57 139.28 -13.71 1.83e+00 2.99e-01 5.63e+01 angle pdb=" C1D BCL 8 102 " pdb=" C2D BCL 8 102 " pdb=" CMD BCL 8 102 " ideal model delta sigma weight residual 125.57 139.06 -13.49 1.83e+00 2.99e-01 5.44e+01 angle pdb=" C1D BCL M 803 " pdb=" C2D BCL M 803 " pdb=" CMD BCL M 803 " ideal model delta sigma weight residual 125.57 139.05 -13.48 1.83e+00 2.99e-01 5.44e+01 angle pdb=" C1D BCL A 703 " pdb=" C2D BCL A 703 " pdb=" CMD BCL A 703 " ideal model delta sigma weight residual 125.57 138.97 -13.40 1.83e+00 2.99e-01 5.37e+01 ... (remaining 33234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 13144 35.96 - 71.92: 650 71.92 - 107.89: 127 107.89 - 143.85: 52 143.85 - 179.81: 8 Dihedral angle restraints: 13981 sinusoidal: 7399 harmonic: 6582 Sorted by residual: dihedral pdb=" C1 BCL L 309 " pdb=" C2 BCL L 309 " pdb=" C3 BCL L 309 " pdb=" C5 BCL L 309 " ideal model delta sinusoidal sigma weight residual -180.00 -0.66 -179.34 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" CBD BCL L 301 " pdb=" CGD BCL L 301 " pdb=" O2D BCL L 301 " pdb=" CED BCL L 301 " ideal model delta sinusoidal sigma weight residual 180.00 135.34 44.66 1 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CBD BCL M 803 " pdb=" CGD BCL M 803 " pdb=" O2D BCL M 803 " pdb=" CED BCL M 803 " ideal model delta sinusoidal sigma weight residual 180.00 137.91 42.09 1 5.00e+00 4.00e-02 9.90e+01 ... (remaining 13978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2645 0.057 - 0.115: 511 0.115 - 0.172: 123 0.172 - 0.230: 41 0.230 - 0.287: 15 Chirality restraints: 3335 Sorted by residual: chirality pdb=" C05 PGV Q 103 " pdb=" C04 PGV Q 103 " pdb=" C06 PGV Q 103 " pdb=" O05 PGV Q 103 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C05 PGV L 305 " pdb=" C04 PGV L 305 " pdb=" C06 PGV L 305 " pdb=" O05 PGV L 305 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C05 PGV X 101 " pdb=" C04 PGV X 101 " pdb=" C06 PGV X 101 " pdb=" O05 PGV X 101 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3332 not shown) Planarity restraints: 3930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A BCL 8 102 " -0.080 3.20e-02 9.77e+02 2.46e-01 2.95e+02 pdb=" C4A BCL 8 102 " -0.035 3.20e-02 9.77e+02 pdb=" CHA BCL 8 102 " 0.264 3.20e-02 9.77e+02 pdb=" CHB BCL 8 102 " 0.252 3.20e-02 9.77e+02 pdb=" NA BCL 8 102 " -0.402 3.20e-02 9.77e+02 delta sigma weight rms_deltas residual plane pdb=" C1 BPH M 804 " 0.178 2.00e-02 2.50e+03 1.47e-01 2.70e+02 pdb=" C2 BPH M 804 " -0.223 2.00e-02 2.50e+03 pdb=" C3 BPH M 804 " -0.077 2.00e-02 2.50e+03 pdb=" C4 BPH M 804 " -0.020 2.00e-02 2.50e+03 pdb=" C5 BPH M 804 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL W 101 " -0.271 3.00e-02 1.11e+03 2.17e-01 2.61e+02 pdb=" CBA BCL W 101 " -0.178 3.00e-02 1.11e+03 pdb=" CGA BCL W 101 " 0.069 3.00e-02 1.11e+03 pdb=" O1A BCL W 101 " 0.027 3.00e-02 1.11e+03 pdb=" O2A BCL W 101 " 0.353 3.00e-02 1.11e+03 ... (remaining 3927 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 148 2.57 - 3.15: 17150 3.15 - 3.74: 36713 3.74 - 4.32: 56462 4.32 - 4.90: 91637 Nonbonded interactions: 202110 Sorted by model distance: nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 805 " model vdw 1.988 2.260 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 805 " model vdw 2.084 2.260 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE M 805 " model vdw 2.167 2.340 nonbonded pdb=" O1B LMT H 301 " pdb=" O6' LMT H 301 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR D 41 " pdb=" O ARG E 45 " model vdw 2.191 3.040 ... (remaining 202105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '1' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain '3' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain '5' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain '7' and (resid 4 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'D' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 54)) selection = (chain 'F' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'I' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'K' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'O' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'Q' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'S' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'V' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'Y' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) } ncs_group { reference = (chain '2' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '4' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '6' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '8' and resid 11 through 48) selection = (chain 'B' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'E' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'G' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'J' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'N' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'P' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'R' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'T' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'W' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'Z' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 58.390 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.179 24319 Z= 0.982 Angle : 1.896 18.619 33239 Z= 0.803 Chirality : 0.056 0.287 3335 Planarity : 0.016 0.246 3930 Dihedral : 22.127 179.811 9751 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.93 % Allowed : 4.72 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.03 (0.17), residues: 2199 helix: 0.29 (0.12), residues: 1500 sheet: -0.43 (1.15), residues: 24 loop : -0.30 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 252 HIS 0.008 0.001 HIS L 153 PHE 0.011 0.001 PHE H 10 TYR 0.011 0.002 TYR R 8 ARG 0.005 0.001 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 350 time to evaluate : 2.135 Fit side-chains REVERT: L 102 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8799 (mt) REVERT: L 248 MET cc_start: 0.8663 (mmm) cc_final: 0.8450 (mmm) REVERT: M 263 GLU cc_start: 0.8522 (tt0) cc_final: 0.8095 (tt0) REVERT: M 292 ASP cc_start: 0.7462 (p0) cc_final: 0.7245 (p0) REVERT: H 30 TYR cc_start: 0.8642 (t80) cc_final: 0.8438 (t80) REVERT: H 52 ASN cc_start: 0.8675 (p0) cc_final: 0.8259 (p0) REVERT: H 106 LYS cc_start: 0.7658 (mttm) cc_final: 0.7305 (mtmt) REVERT: H 128 HIS cc_start: 0.7854 (m-70) cc_final: 0.7499 (m170) REVERT: H 182 GLU cc_start: 0.7962 (tt0) cc_final: 0.7622 (tt0) REVERT: A 6 LYS cc_start: 0.8522 (mtpp) cc_final: 0.8279 (mtmt) REVERT: B 11 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8261 (mp) REVERT: B 17 GLN cc_start: 0.8325 (mt0) cc_final: 0.7954 (mt0) REVERT: G 14 GLU cc_start: 0.7372 (pm20) cc_final: 0.7151 (pm20) REVERT: I 5 TYR cc_start: 0.8568 (p90) cc_final: 0.8353 (p90) REVERT: K 12 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7666 (t0) REVERT: O 15 ARG cc_start: 0.7071 (tmm160) cc_final: 0.6441 (mtp85) REVERT: O 45 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7099 (mm-30) REVERT: P 25 SER cc_start: 0.8657 (t) cc_final: 0.8374 (p) REVERT: P 29 LEU cc_start: 0.8610 (tp) cc_final: 0.7945 (tp) REVERT: Q 5 TYR cc_start: 0.8225 (p90) cc_final: 0.7915 (p90) REVERT: Q 6 LYS cc_start: 0.8043 (mttm) cc_final: 0.7751 (mttt) REVERT: V 6 LYS cc_start: 0.7624 (mmmm) cc_final: 0.7071 (mmmt) REVERT: V 45 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7594 (mm-30) REVERT: Z 15 GLN cc_start: 0.7782 (mt0) cc_final: 0.7456 (mt0) REVERT: Z 45 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7906 (ttt-90) REVERT: 2 18 GLU cc_start: 0.7005 (tp30) cc_final: 0.6530 (tp30) REVERT: 3 5 TYR cc_start: 0.7517 (p90) cc_final: 0.7273 (p90) REVERT: 3 27 LEU cc_start: 0.8707 (tp) cc_final: 0.8470 (tp) REVERT: 5 18 VAL cc_start: 0.8043 (t) cc_final: 0.7841 (t) REVERT: 5 30 MET cc_start: 0.8055 (ttp) cc_final: 0.7843 (ttp) REVERT: 6 13 ASP cc_start: 0.6134 (t0) cc_final: 0.5274 (t0) REVERT: 6 15 GLN cc_start: 0.5722 (mt0) cc_final: 0.5115 (mm110) REVERT: 7 30 MET cc_start: 0.7313 (mmt) cc_final: 0.7023 (mmt) REVERT: 7 51 TYR cc_start: 0.7620 (m-80) cc_final: 0.7362 (m-80) REVERT: U 24 MET cc_start: 0.7676 (ptp) cc_final: 0.7325 (ptp) outliers start: 36 outliers final: 19 residues processed: 378 average time/residue: 1.2084 time to fit residues: 530.4208 Evaluate side-chains 321 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 298 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 272 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Z residue 45 ARG Chi-restraints excluded: chain 7 residue 34 ILE Chi-restraints excluded: chain X residue 17 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 301 HIS G 17 GLN K 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 17 GLN V 20 GLN 5 52 ASN X 66 ASN U 51 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24319 Z= 0.209 Angle : 0.751 14.556 33239 Z= 0.292 Chirality : 0.041 0.478 3335 Planarity : 0.004 0.054 3930 Dihedral : 19.897 179.396 5879 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.95 % Allowed : 10.45 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.93 (0.18), residues: 2199 helix: 1.96 (0.13), residues: 1517 sheet: 0.38 (0.95), residues: 34 loop : -0.26 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 252 HIS 0.006 0.001 HIS M 182 PHE 0.013 0.001 PHE M 189 TYR 0.011 0.001 TYR M 198 ARG 0.004 0.000 ARG L 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 314 time to evaluate : 2.286 Fit side-chains REVERT: L 102 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8642 (mt) REVERT: L 248 MET cc_start: 0.8572 (mmm) cc_final: 0.8349 (mmm) REVERT: M 86 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8636 (tp) REVERT: M 210 TYR cc_start: 0.8709 (m-10) cc_final: 0.8458 (m-10) REVERT: M 216 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8719 (t80) REVERT: H 30 TYR cc_start: 0.8695 (t80) cc_final: 0.8431 (t80) REVERT: H 52 ASN cc_start: 0.8646 (p0) cc_final: 0.8164 (p0) REVERT: H 106 LYS cc_start: 0.7726 (mttm) cc_final: 0.7366 (mtmt) REVERT: H 128 HIS cc_start: 0.7842 (m-70) cc_final: 0.7540 (m170) REVERT: H 182 GLU cc_start: 0.7920 (tt0) cc_final: 0.7550 (tt0) REVERT: B 11 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8209 (mp) REVERT: B 17 GLN cc_start: 0.8226 (mt0) cc_final: 0.7942 (mt0) REVERT: B 24 MET cc_start: 0.8109 (tpp) cc_final: 0.7806 (mmt) REVERT: G 6 LEU cc_start: 0.3712 (OUTLIER) cc_final: 0.3253 (mt) REVERT: G 43 ILE cc_start: 0.8472 (mt) cc_final: 0.8260 (mm) REVERT: K 6 LYS cc_start: 0.8714 (mmtp) cc_final: 0.8487 (mmtp) REVERT: N 24 MET cc_start: 0.8124 (mmp) cc_final: 0.7601 (mmt) REVERT: O 45 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6958 (mm-30) REVERT: P 29 LEU cc_start: 0.8486 (tp) cc_final: 0.7833 (tp) REVERT: Q 3 LYS cc_start: 0.8116 (mttp) cc_final: 0.7498 (mttp) REVERT: S 3 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8140 (mtpp) REVERT: Z 15 GLN cc_start: 0.7700 (mt0) cc_final: 0.7344 (mt0) REVERT: 3 5 TYR cc_start: 0.7327 (p90) cc_final: 0.7036 (p90) REVERT: 5 53 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7760 (mtm180) REVERT: 6 11 LEU cc_start: 0.6732 (mm) cc_final: 0.6309 (mp) REVERT: 6 13 ASP cc_start: 0.6076 (t0) cc_final: 0.5554 (t70) REVERT: 6 15 GLN cc_start: 0.5961 (mt0) cc_final: 0.5299 (mm110) REVERT: 7 51 TYR cc_start: 0.7619 (m-80) cc_final: 0.7387 (m-80) REVERT: 8 39 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7765 (tp) REVERT: X 29 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8057 (ttmt) REVERT: X 53 ARG cc_start: 0.6962 (mtm110) cc_final: 0.6634 (mtt90) REVERT: U 24 MET cc_start: 0.7621 (ptp) cc_final: 0.7293 (ptp) outliers start: 55 outliers final: 20 residues processed: 345 average time/residue: 1.1367 time to fit residues: 460.8578 Evaluate side-chains 314 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 286 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain 2 residue 11 LEU Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 5 residue 7 ILE Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain U residue 13 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 28 ASN H 44 ASN F 20 GLN O 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 24319 Z= 0.329 Angle : 0.802 18.480 33239 Z= 0.313 Chirality : 0.042 0.501 3335 Planarity : 0.004 0.055 3930 Dihedral : 18.779 179.831 5861 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.59 % Allowed : 12.33 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.83 (0.17), residues: 2199 helix: 1.95 (0.13), residues: 1517 sheet: 0.36 (0.92), residues: 34 loop : -0.48 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 252 HIS 0.008 0.002 HIS L 153 PHE 0.016 0.002 PHE H 20 TYR 0.014 0.002 TYR R 8 ARG 0.006 0.001 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 298 time to evaluate : 2.236 Fit side-chains REVERT: L 102 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8710 (mt) REVERT: L 248 MET cc_start: 0.8617 (mmm) cc_final: 0.8381 (mmm) REVERT: M 216 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8845 (t80) REVERT: H 30 TYR cc_start: 0.8703 (t80) cc_final: 0.8438 (t80) REVERT: H 128 HIS cc_start: 0.7861 (m-70) cc_final: 0.7621 (m170) REVERT: H 182 GLU cc_start: 0.7924 (tt0) cc_final: 0.7541 (tt0) REVERT: B 11 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8257 (mp) REVERT: B 17 GLN cc_start: 0.8265 (mt0) cc_final: 0.7955 (mt0) REVERT: B 24 MET cc_start: 0.8214 (tpp) cc_final: 0.7805 (mmt) REVERT: G 43 ILE cc_start: 0.8493 (mt) cc_final: 0.8270 (mm) REVERT: J 35 ILE cc_start: 0.8730 (mt) cc_final: 0.8506 (mt) REVERT: O 45 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6984 (mm-30) REVERT: P 29 LEU cc_start: 0.8568 (tp) cc_final: 0.7913 (tp) REVERT: Q 3 LYS cc_start: 0.8131 (mttp) cc_final: 0.7530 (mttt) REVERT: Q 5 TYR cc_start: 0.8364 (p90) cc_final: 0.8035 (p90) REVERT: Q 20 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7464 (mm-40) REVERT: S 3 LYS cc_start: 0.8509 (ttmm) cc_final: 0.8237 (mtpp) REVERT: Y 36 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8893 (mt) REVERT: Z 15 GLN cc_start: 0.7854 (mt0) cc_final: 0.7547 (mt0) REVERT: 3 5 TYR cc_start: 0.7358 (p90) cc_final: 0.7059 (p90) REVERT: 5 30 MET cc_start: 0.7927 (ttp) cc_final: 0.7640 (ttp) REVERT: 5 51 TYR cc_start: 0.8149 (m-80) cc_final: 0.7427 (m-80) REVERT: 5 53 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.5507 (mpp-170) REVERT: 6 13 ASP cc_start: 0.6013 (t0) cc_final: 0.5310 (t70) REVERT: 6 15 GLN cc_start: 0.6019 (mt0) cc_final: 0.5266 (mm110) REVERT: 8 24 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6992 (mmt) REVERT: X 53 ARG cc_start: 0.7021 (mtm110) cc_final: 0.6644 (mtt90) REVERT: U 24 MET cc_start: 0.7608 (ptp) cc_final: 0.7407 (ptp) outliers start: 67 outliers final: 37 residues processed: 338 average time/residue: 1.1523 time to fit residues: 457.0521 Evaluate side-chains 324 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 280 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 272 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 36 LEU Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 3 residue 29 VAL Chi-restraints excluded: chain 5 residue 7 ILE Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 8 residue 24 MET Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain U residue 12 MET Chi-restraints excluded: chain U residue 13 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 186 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN O 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 20 GLN 5 52 ASN X 66 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24319 Z= 0.287 Angle : 0.756 18.467 33239 Z= 0.293 Chirality : 0.041 0.511 3335 Planarity : 0.004 0.054 3930 Dihedral : 18.259 179.808 5860 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.86 % Allowed : 13.56 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.95 (0.17), residues: 2199 helix: 2.07 (0.12), residues: 1518 sheet: 0.41 (0.92), residues: 34 loop : -0.55 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 252 HIS 0.007 0.001 HIS L 153 PHE 0.022 0.001 PHE U 27 TYR 0.014 0.002 TYR O 5 ARG 0.003 0.001 ARG 6 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 301 time to evaluate : 2.141 Fit side-chains REVERT: L 102 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8645 (mt) REVERT: M 20 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7596 (mtp) REVERT: M 216 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8773 (t80) REVERT: H 30 TYR cc_start: 0.8709 (t80) cc_final: 0.8440 (t80) REVERT: H 43 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6499 (mm-30) REVERT: H 52 ASN cc_start: 0.8769 (p0) cc_final: 0.8376 (p0) REVERT: H 122 GLU cc_start: 0.7265 (tt0) cc_final: 0.6928 (tt0) REVERT: H 128 HIS cc_start: 0.7892 (m-70) cc_final: 0.7678 (m170) REVERT: H 182 GLU cc_start: 0.7911 (tt0) cc_final: 0.7530 (tt0) REVERT: B 17 GLN cc_start: 0.8123 (mt0) cc_final: 0.7817 (mt0) REVERT: B 24 MET cc_start: 0.8193 (tpp) cc_final: 0.7772 (mmt) REVERT: F 15 ARG cc_start: 0.8143 (mtt-85) cc_final: 0.7817 (mtp-110) REVERT: G 43 ILE cc_start: 0.8474 (mt) cc_final: 0.8266 (mm) REVERT: J 35 ILE cc_start: 0.8734 (mt) cc_final: 0.8530 (mt) REVERT: O 6 LYS cc_start: 0.8261 (mtmm) cc_final: 0.8008 (mttp) REVERT: O 45 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6970 (mm-30) REVERT: P 29 LEU cc_start: 0.8554 (tp) cc_final: 0.7896 (tp) REVERT: Q 3 LYS cc_start: 0.8126 (mttp) cc_final: 0.7525 (mttt) REVERT: Q 5 TYR cc_start: 0.8342 (p90) cc_final: 0.7989 (p90) REVERT: S 3 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8226 (mtpp) REVERT: Z 15 GLN cc_start: 0.7962 (mt0) cc_final: 0.7605 (mt0) REVERT: 3 5 TYR cc_start: 0.7346 (p90) cc_final: 0.7055 (p90) REVERT: 5 15 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.5071 (tmt170) REVERT: 5 30 MET cc_start: 0.7918 (ttp) cc_final: 0.7650 (ttp) REVERT: 5 53 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7664 (mtm180) REVERT: 6 15 GLN cc_start: 0.6074 (mt0) cc_final: 0.5274 (mm110) REVERT: 8 39 LEU cc_start: 0.7916 (tt) cc_final: 0.7611 (tp) REVERT: X 53 ARG cc_start: 0.6977 (mtm110) cc_final: 0.6656 (mtt90) REVERT: U 24 MET cc_start: 0.7687 (ptp) cc_final: 0.7438 (ptp) REVERT: U 27 PHE cc_start: 0.8093 (t80) cc_final: 0.7820 (t80) outliers start: 72 outliers final: 38 residues processed: 341 average time/residue: 1.1211 time to fit residues: 448.7674 Evaluate side-chains 326 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 282 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 272 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 7 ILE Chi-restraints excluded: chain 5 residue 15 ARG Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 7 residue 52 ASN Chi-restraints excluded: chain 7 residue 54 VAL Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain U residue 13 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN O 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24319 Z= 0.270 Angle : 0.748 18.109 33239 Z= 0.289 Chirality : 0.040 0.522 3335 Planarity : 0.004 0.056 3930 Dihedral : 17.976 179.809 5858 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.70 % Allowed : 14.31 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.17), residues: 2199 helix: 2.13 (0.12), residues: 1518 sheet: 0.45 (0.93), residues: 34 loop : -0.56 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 252 HIS 0.007 0.001 HIS L 153 PHE 0.015 0.001 PHE H 20 TYR 0.014 0.002 TYR M 210 ARG 0.003 0.000 ARG O 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 295 time to evaluate : 2.142 Fit side-chains REVERT: L 102 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8631 (mt) REVERT: M 20 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7633 (mtp) REVERT: M 60 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8225 (mm) REVERT: M 216 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8755 (t80) REVERT: M 263 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: H 30 TYR cc_start: 0.8713 (t80) cc_final: 0.8451 (t80) REVERT: H 43 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6445 (mm-30) REVERT: H 52 ASN cc_start: 0.8792 (p0) cc_final: 0.8387 (p0) REVERT: H 182 GLU cc_start: 0.7918 (tt0) cc_final: 0.7525 (tt0) REVERT: H 230 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6719 (mt-10) REVERT: B 17 GLN cc_start: 0.8127 (mt0) cc_final: 0.7788 (mt0) REVERT: B 24 MET cc_start: 0.8187 (tpp) cc_final: 0.7780 (mmt) REVERT: G 43 ILE cc_start: 0.8466 (mt) cc_final: 0.8262 (mm) REVERT: J 35 ILE cc_start: 0.8742 (mt) cc_final: 0.8527 (mt) REVERT: N 24 MET cc_start: 0.8232 (mmt) cc_final: 0.7583 (mmt) REVERT: O 45 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6966 (mm-30) REVERT: P 29 LEU cc_start: 0.8531 (tp) cc_final: 0.7895 (tp) REVERT: Q 3 LYS cc_start: 0.8119 (mttp) cc_final: 0.7533 (mttt) REVERT: Q 5 TYR cc_start: 0.8294 (p90) cc_final: 0.7944 (p90) REVERT: S 3 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8220 (mtpp) REVERT: Z 15 GLN cc_start: 0.7976 (mt0) cc_final: 0.7615 (mt0) REVERT: 3 5 TYR cc_start: 0.7393 (p90) cc_final: 0.7099 (p90) REVERT: 5 15 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.5084 (tmt170) REVERT: 5 30 MET cc_start: 0.7923 (ttp) cc_final: 0.7672 (ttp) REVERT: 5 53 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7652 (mtm180) REVERT: 6 15 GLN cc_start: 0.6064 (mt0) cc_final: 0.5254 (mm110) REVERT: 8 39 LEU cc_start: 0.8048 (tt) cc_final: 0.7781 (tp) REVERT: X 53 ARG cc_start: 0.6939 (mtm110) cc_final: 0.6600 (mtt90) REVERT: U 24 MET cc_start: 0.7682 (ptp) cc_final: 0.7439 (ptp) REVERT: U 27 PHE cc_start: 0.8003 (t80) cc_final: 0.7772 (t80) outliers start: 69 outliers final: 46 residues processed: 338 average time/residue: 1.1178 time to fit residues: 442.9867 Evaluate side-chains 329 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 275 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain M residue 272 MET Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 3 residue 29 VAL Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 7 ILE Chi-restraints excluded: chain 5 residue 15 ARG Chi-restraints excluded: chain 5 residue 40 SER Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 5 residue 54 VAL Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 7 residue 52 ASN Chi-restraints excluded: chain 7 residue 54 VAL Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain U residue 12 MET Chi-restraints excluded: chain U residue 13 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 chunk 173 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 109 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: