Starting phenix.real_space_refine on Sat Feb 17 21:59:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yq7_6828/02_2024/5yq7_6828_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yq7_6828/02_2024/5yq7_6828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yq7_6828/02_2024/5yq7_6828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yq7_6828/02_2024/5yq7_6828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yq7_6828/02_2024/5yq7_6828_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yq7_6828/02_2024/5yq7_6828_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 Fe 5 7.16 5 Mg 48 5.21 5 S 51 5.16 5 C 14179 2.51 5 N 2791 2.21 5 O 2935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M ARG 410": "NH1" <-> "NH2" Residue "M TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 503": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20009 Number of models: 1 Model: "" Number of chains: 68 Chain: "E" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 325 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 325 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "0" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2292 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 17, 'TRANS': 291} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "8" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "6" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "4" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 319 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "2" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 326 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "K" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 325 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2041 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 21, 'TRANS': 271} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 125 Chain: "I" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "W" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 312 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "U" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "T" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "S" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 326 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "Q" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 318 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "O" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 325 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "V" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 257 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "N" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 260 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "9" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "7" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "5" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "3" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 260 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "1" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 245 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "Y" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 125 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'UNK:plan-1': 25} Unresolved non-hydrogen planarities: 25 Chain: "X" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 115 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "M" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 16, 'TRANS': 288} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 76 Chain: "E" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 266 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'MQE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "8" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'HEM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "5" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "1" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 264 Unusual residues: {'BCL': 1, 'BPH': 2, 'MQE': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 10.78, per 1000 atoms: 0.54 Number of scatterers: 20009 At special positions: 0 Unit cell: (137.76, 142.24, 129.92, 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) Fe 5 26.01 S 51 16.00 Mg 48 11.99 O 2935 8.00 N 2791 7.00 C 14179 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=65, symmetry=0 Number of additional bonds: simple=65, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.99 Conformation dependent library (CDL) restraints added in 2.9 seconds 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4026 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 0 sheets defined 57.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'E' and resid 23 through 50 removed outlier: 3.661A pdb=" N ALA E 49 " --> pdb=" O VAL E 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 50 removed outlier: 3.813A pdb=" N ASP B 27 " --> pdb=" O TRP B 23 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain '0' and resid 23 through 50 removed outlier: 3.781A pdb=" N LYS 0 31 " --> pdb=" O ASP 0 27 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TRP 0 50 " --> pdb=" O LEU 0 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 32 Proline residue: L 17 - end of helix removed outlier: 4.049A pdb=" N SER L 26 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ALA L 31 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 45 removed outlier: 3.738A pdb=" N ARG L 45 " --> pdb=" O GLU L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 92 Processing helix chain 'L' and resid 124 through 149 Processing helix chain 'L' and resid 155 through 171 removed outlier: 3.704A pdb=" N ALA L 162 " --> pdb=" O ILE L 158 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL L 163 " --> pdb=" O ALA L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 177 removed outlier: 3.604A pdb=" N ALA L 177 " --> pdb=" O LEU L 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 173 through 177' Processing helix chain 'L' and resid 192 through 202 removed outlier: 4.296A pdb=" N VAL L 196 " --> pdb=" O HIS L 192 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR L 201 " --> pdb=" O SER L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 235 removed outlier: 3.801A pdb=" N SER L 235 " --> pdb=" O SER L 231 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 252 removed outlier: 3.566A pdb=" N ASN L 252 " --> pdb=" O VAL L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 285 removed outlier: 4.093A pdb=" N ALA L 273 " --> pdb=" O THR L 270 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N SER L 274 " --> pdb=" O GLY L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 296 No H-bonds generated for 'chain 'L' and resid 294 through 296' Processing helix chain 'L' and resid 303 through 305 No H-bonds generated for 'chain 'L' and resid 303 through 305' Processing helix chain '8' and resid 23 through 48 removed outlier: 3.938A pdb=" N ILE 8 38 " --> pdb=" O TYR 8 34 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE 8 39 " --> pdb=" O GLY 8 35 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP 8 48 " --> pdb=" O HIS 8 44 " (cutoff:3.500A) Processing helix chain '6' and resid 23 through 50 removed outlier: 4.754A pdb=" N ILE 6 38 " --> pdb=" O TYR 6 34 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE 6 39 " --> pdb=" O GLY 6 35 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA 6 40 " --> pdb=" O GLY 6 36 " (cutoff:3.500A) Processing helix chain '4' and resid 23 through 50 removed outlier: 3.707A pdb=" N ILE 4 38 " --> pdb=" O TYR 4 34 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE 4 39 " --> pdb=" O GLY 4 35 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TRP 4 48 " --> pdb=" O HIS 4 44 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA 4 49 " --> pdb=" O VAL 4 45 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TRP 4 50 " --> pdb=" O LEU 4 46 " (cutoff:3.500A) Processing helix chain '2' and resid 23 through 47 removed outlier: 3.515A pdb=" N TYR 2 34 " --> pdb=" O VAL 2 30 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY 2 35 " --> pdb=" O LYS 2 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 48 removed outlier: 3.988A pdb=" N TRP K 48 " --> pdb=" O HIS K 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 34 removed outlier: 3.728A pdb=" N GLY C 25 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ILE C 27 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 49 Proline residue: C 48 - end of helix Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 73 through 78 removed outlier: 4.240A pdb=" N ALA C 76 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 84 No H-bonds generated for 'chain 'C' and resid 81 through 84' Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 136 through 156 removed outlier: 3.595A pdb=" N MET C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER C 149 " --> pdb=" O MET C 145 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA C 150 " --> pdb=" O MET C 146 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLN C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 235 removed outlier: 3.884A pdb=" N ALA C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 274 Processing helix chain 'I' and resid 23 through 47 Processing helix chain 'G' and resid 23 through 48 removed outlier: 3.898A pdb=" N LYS G 31 " --> pdb=" O ASP G 27 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TRP G 48 " --> pdb=" O HIS G 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 47 removed outlier: 3.592A pdb=" N LYS W 31 " --> pdb=" O ASP W 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 49 removed outlier: 3.636A pdb=" N TRP U 48 " --> pdb=" O HIS U 44 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA U 49 " --> pdb=" O VAL U 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 33 Processing helix chain 'S' and resid 23 through 50 removed outlier: 3.635A pdb=" N ILE S 42 " --> pdb=" O ILE S 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 48 removed outlier: 3.829A pdb=" N ASP Q 27 " --> pdb=" O TRP Q 23 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP Q 48 " --> pdb=" O HIS Q 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 47 Processing helix chain 'V' and resid 9 through 31 Processing helix chain 'R' and resid 9 through 32 Processing helix chain 'P' and resid 9 through 33 removed outlier: 3.636A pdb=" N SER P 15 " --> pdb=" O SER P 11 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER P 33 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 33 Processing helix chain 'J' and resid 9 through 33 removed outlier: 4.009A pdb=" N SER J 15 " --> pdb=" O SER J 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 32 removed outlier: 3.667A pdb=" N VAL H 12 " --> pdb=" O PHE H 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 removed outlier: 4.169A pdb=" N VAL F 13 " --> pdb=" O ARG F 9 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL F 14 " --> pdb=" O THR F 10 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER F 15 " --> pdb=" O SER F 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.581A pdb=" N VAL A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain '9' and resid 9 through 33 removed outlier: 3.545A pdb=" N VAL 9 13 " --> pdb=" O ARG 9 9 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 32 Processing helix chain '5' and resid 9 through 33 removed outlier: 3.716A pdb=" N THR 5 16 " --> pdb=" O VAL 5 12 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU 5 31 " --> pdb=" O HIS 5 27 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 33 Processing helix chain '1' and resid 8 through 30 removed outlier: 3.621A pdb=" N VAL 1 14 " --> pdb=" O THR 1 10 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER 1 15 " --> pdb=" O SER 1 11 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR 1 16 " --> pdb=" O VAL 1 12 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU 1 17 " --> pdb=" O VAL 1 13 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 24 removed outlier: 5.087A pdb=" N UNK Y 9 " --> pdb=" O UNK Y 6 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N UNK Y 10 " --> pdb=" O UNK Y 7 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N UNK Y 13 " --> pdb=" O UNK Y 10 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N UNK Y 14 " --> pdb=" O UNK Y 11 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N UNK Y 18 " --> pdb=" O UNK Y 15 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N UNK Y 19 " --> pdb=" O UNK Y 16 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N UNK Y 23 " --> pdb=" O UNK Y 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 22 Processing helix chain 'M' and resid 362 through 365 No H-bonds generated for 'chain 'M' and resid 362 through 365' Processing helix chain 'M' and resid 380 through 399 removed outlier: 3.685A pdb=" N ASP M 396 " --> pdb=" O ILE M 392 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG M 399 " --> pdb=" O VAL M 395 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 410 Processing helix chain 'M' and resid 439 through 462 Processing helix chain 'M' and resid 469 through 484 removed outlier: 3.659A pdb=" N ALA M 474 " --> pdb=" O ALA M 470 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU M 479 " --> pdb=" O SER M 475 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR M 480 " --> pdb=" O ALA M 476 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE M 481 " --> pdb=" O LEU M 477 " (cutoff:3.500A) Processing helix chain 'M' and resid 505 through 516 removed outlier: 4.372A pdb=" N ASN M 510 " --> pdb=" O LEU M 506 " (cutoff:3.500A) Processing helix chain 'M' and resid 519 through 521 No H-bonds generated for 'chain 'M' and resid 519 through 521' Processing helix chain 'M' and resid 523 through 551 removed outlier: 4.771A pdb=" N LYS M 551 " --> pdb=" O VAL M 547 " (cutoff:3.500A) Processing helix chain 'M' and resid 566 through 577 removed outlier: 3.632A pdb=" N LEU M 573 " --> pdb=" O GLN M 569 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE M 574 " --> pdb=" O ARG M 570 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP M 575 " --> pdb=" O ALA M 571 " (cutoff:3.500A) Processing helix chain 'M' and resid 588 through 609 removed outlier: 4.229A pdb=" N THR M 599 " --> pdb=" O PHE M 595 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA M 600 " --> pdb=" O ALA M 596 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU M 609 " --> pdb=" O ILE M 605 " (cutoff:3.500A) Processing helix chain 'M' and resid 620 through 622 No H-bonds generated for 'chain 'M' and resid 620 through 622' 874 hydrogen bonds defined for protein. 2499 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: 4.37 Time building geometry restraints manager: 9.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.36: 5403 1.36 - 1.56: 15242 1.56 - 1.77: 1 1.77 - 1.97: 84 1.97 - 2.17: 206 Bond restraints: 20936 Sorted by residual: bond pdb=" CAX KGD H 102 " pdb=" CAY KGD H 102 " ideal model delta sigma weight residual 1.336 1.549 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" CAJ KGD 5 101 " pdb=" CAL KGD 5 101 " ideal model delta sigma weight residual 1.343 1.547 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" CAX KGD 5 101 " pdb=" CAY KGD 5 101 " ideal model delta sigma weight residual 1.336 1.539 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" CAV MQE L1004 " pdb=" CBF MQE L1004 " ideal model delta sigma weight residual 1.336 1.539 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" CAZ MQE L1004 " pdb=" CBI MQE L1004 " ideal model delta sigma weight residual 1.336 1.538 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 20931 not shown) Histogram of bond angle deviations from ideal: 68.40 - 90.33: 183 90.33 - 112.25: 11348 112.25 - 134.18: 17809 134.18 - 156.10: 57 156.10 - 178.03: 106 Bond angle restraints: 29503 Sorted by residual: angle pdb=" C4 BCL W 101 " pdb=" C3 BCL W 101 " pdb=" C5 BCL W 101 " ideal model delta sigma weight residual 114.06 68.40 45.65 3.27e+00 9.35e-02 1.95e+02 angle pdb=" C4 BCL U 101 " pdb=" C3 BCL U 101 " pdb=" C5 BCL U 101 " ideal model delta sigma weight residual 114.06 68.96 45.10 3.27e+00 9.35e-02 1.90e+02 angle pdb=" C2 BCL U 101 " pdb=" C3 BCL U 101 " pdb=" C5 BCL U 101 " ideal model delta sigma weight residual 120.75 160.88 -40.13 3.08e+00 1.05e-01 1.69e+02 angle pdb=" C2 BCL W 101 " pdb=" C3 BCL W 101 " pdb=" C5 BCL W 101 " ideal model delta sigma weight residual 120.75 160.40 -39.65 3.08e+00 1.05e-01 1.65e+02 angle pdb=" C2 BCL U 101 " pdb=" C3 BCL U 101 " pdb=" C4 BCL U 101 " ideal model delta sigma weight residual 124.96 91.93 33.04 2.80e+00 1.28e-01 1.39e+02 ... (remaining 29498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 10233 35.99 - 71.98: 181 71.98 - 107.97: 38 107.97 - 143.96: 35 143.96 - 179.95: 3 Dihedral angle restraints: 10490 sinusoidal: 4298 harmonic: 6192 Sorted by residual: dihedral pdb=" C1 BCL 4 101 " pdb=" C2 BCL 4 101 " pdb=" C3 BCL 4 101 " pdb=" C5 BCL 4 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.05 -179.95 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL 2 101 " pdb=" C2 BCL 2 101 " pdb=" C3 BCL 2 101 " pdb=" C5 BCL 2 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.27 179.73 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL L1002 " pdb=" C2 BCL L1002 " pdb=" C3 BCL L1002 " pdb=" C5 BCL L1002 " ideal model delta sinusoidal sigma weight residual -180.00 -0.38 -179.62 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 10487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2744 0.073 - 0.146: 334 0.146 - 0.218: 19 0.218 - 0.291: 3 0.291 - 0.364: 2 Chirality restraints: 3102 Sorted by residual: chirality pdb=" CA PHE H 8 " pdb=" N PHE H 8 " pdb=" C PHE H 8 " pdb=" CB PHE H 8 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CBD BCL B 102 " pdb=" CAD BCL B 102 " pdb=" CGD BCL B 102 " pdb=" CHA BCL B 102 " both_signs ideal model delta sigma weight residual False 2.62 2.33 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C13 BPH M 703 " pdb=" C12 BPH M 703 " pdb=" C14 BPH M 703 " pdb=" C15 BPH M 703 " both_signs ideal model delta sigma weight residual False 2.60 2.84 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3099 not shown) Planarity restraints: 3485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BPH M 703 " 0.010 2.00e-02 2.50e+03 5.93e-02 7.92e+01 pdb=" C1D BPH M 703 " 0.020 2.00e-02 2.50e+03 pdb=" C2D BPH M 703 " -0.027 2.00e-02 2.50e+03 pdb=" C3D BPH M 703 " -0.047 2.00e-02 2.50e+03 pdb=" C4D BPH M 703 " -0.030 2.00e-02 2.50e+03 pdb=" CAD BPH M 703 " 0.132 2.00e-02 2.50e+03 pdb=" CHA BPH M 703 " -0.055 2.00e-02 2.50e+03 pdb=" CHD BPH M 703 " 0.057 2.00e-02 2.50e+03 pdb=" CMD BPH M 703 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH L1003 " 0.005 2.00e-02 2.50e+03 5.01e-02 5.64e+01 pdb=" C1D BPH L1003 " 0.023 2.00e-02 2.50e+03 pdb=" C2D BPH L1003 " -0.019 2.00e-02 2.50e+03 pdb=" C3D BPH L1003 " -0.026 2.00e-02 2.50e+03 pdb=" C4D BPH L1003 " -0.024 2.00e-02 2.50e+03 pdb=" CAD BPH L1003 " 0.108 2.00e-02 2.50e+03 pdb=" CHA BPH L1003 " -0.054 2.00e-02 2.50e+03 pdb=" CHD BPH L1003 " 0.047 2.00e-02 2.50e+03 pdb=" CMD BPH L1003 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BPH L1003 " -0.004 2.00e-02 2.50e+03 4.65e-02 4.86e+01 pdb=" C1B BPH L1003 " -0.025 2.00e-02 2.50e+03 pdb=" C2B BPH L1003 " 0.015 2.00e-02 2.50e+03 pdb=" C3B BPH L1003 " -0.005 2.00e-02 2.50e+03 pdb=" C4B BPH L1003 " 0.031 2.00e-02 2.50e+03 pdb=" CAB BPH L1003 " -0.085 2.00e-02 2.50e+03 pdb=" CHB BPH L1003 " -0.049 2.00e-02 2.50e+03 pdb=" CHC BPH L1003 " 0.044 2.00e-02 2.50e+03 pdb=" CMB BPH L1003 " 0.078 2.00e-02 2.50e+03 ... (remaining 3482 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 21 2.21 - 2.89: 7109 2.89 - 3.56: 28567 3.56 - 4.23: 39596 4.23 - 4.90: 65750 Nonbonded interactions: 141043 Sorted by model distance: nonbonded pdb=" CE1 HIS L 192 " pdb="MG BCL L1001 " model vdw 1.542 3.130 nonbonded pdb=" CE1 HIS G 44 " pdb="MG BCL G 101 " model vdw 1.689 3.130 nonbonded pdb=" CE1 HIS Q 44 " pdb="MG BCL Q 101 " model vdw 1.704 3.130 nonbonded pdb=" CE1 HIS C 244 " pdb="FE HEM C 503 " model vdw 1.729 3.220 nonbonded pdb=" OE2 GLU M 557 " pdb="FE FE L1005 " model vdw 1.784 2.260 ... (remaining 141038 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 '0' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 54 or resid 101 through 102)) selection = (chain '2' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 54 or resid 101 through 102)) selection = (chain '4' and (resid 11 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 33 or (resid 34 and (name N or nam \ e CA or name C or name O or name CB )) or resid 35 through 36 or (resid 37 and ( \ name N or name CA or name C or name O or name CB )) or resid 38 through 54 or re \ sid 101 through 102)) selection = (chain '6' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 54 or resid 101 through 102)) selection = (chain '8' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 54 or resid 101 through 102)) selection = (chain 'B' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 33 or (resid 34 and (na \ me N or name CA or name C or name O or name CB )) or resid 35 through 36 or (res \ id 37 and (name N or name CA or name C or name O or name CB )) or resid 38 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 54 or resid 101 through 102)) selection = (chain 'E' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 33 or (resid 34 and (na \ me N or name CA or name C or name O or name CB )) or resid 35 through 36 or (res \ id 37 and (name N or name CA or name C or name O or name CB )) or resid 38 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 54 or resid 101 through 102)) selection = (chain 'G' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 54 or resid 101 through 102)) selection = (chain 'I' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 54 or resid 101 through 102)) selection = (chain 'K' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 33 or (resid 34 and (na \ me N or name CA or name C or name O or name CB )) or resid 35 through 36 or (res \ id 37 and (name N or name CA or name C or name O or name CB )) or resid 38 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 54 or resid 101 through 102)) selection = (chain 'O' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 33 or (resid 34 and (na \ me N or name CA or name C or name O or name CB )) or resid 35 through 36 or (res \ id 37 and (name N or name CA or name C or name O or name CB )) or resid 38 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 54 or resid 101 through 102)) selection = (chain 'Q' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 36 or (resid 37 and (na \ me N or name CA or name C or name O or name CB )) or resid 38 through 45 or (res \ id 46 and (name N or name CA or name C or name O or name CB )) or resid 47 throu \ gh 54 or resid 101 through 102)) selection = (chain 'S' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 54 or resid 101 through 102)) selection = (chain 'U' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 54 or resid 101 through 102)) selection = (chain 'W' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 54 or resid 101 through \ 102)) } ncs_group { reference = (chain '1' and (resid 5 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 40)) selection = (chain '3' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain '5' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain '7' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain '9' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'A' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'D' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'F' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'H' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'J' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 40)) selection = (chain 'N' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'P' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'R' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 throug \ h 40 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'T' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'V' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 21 or (resid 22 through 23 and (name N or name C \ A or name C or name O or name CB )) or resid 24 through 35 or (resid 36 and (nam \ e N or name CA or name C or name O or name CB )) or resid 37 through 38 or (resi \ d 39 through 40 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'X' selection = (chain 'Y' and resid 3 through 25) } 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: 0.490 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: 0.010 Extract box with map and model: 2.640 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 51.170 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 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 0.213 20936 Z= 0.875 Angle : 1.763 45.655 29503 Z= 0.668 Chirality : 0.049 0.364 3102 Planarity : 0.005 0.078 3485 Dihedral : 17.920 179.948 6464 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.65 % Favored : 85.15 % Rotamer: Outliers : 0.14 % Allowed : 3.54 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.20 % 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: -4.34 (0.15), residues: 2041 helix: -1.59 (0.12), residues: 1222 sheet: None (None), residues: 0 loop : -5.04 (0.16), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP M 577 HIS 0.024 0.002 HIS A 27 PHE 0.026 0.002 PHE C 242 TYR 0.031 0.003 TYR 6 34 ARG 0.005 0.001 ARG M 410 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 776 time to evaluate : 1.983 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: L 19 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7866 (tm-30) REVERT: L 143 GLN cc_start: 0.9089 (mt0) cc_final: 0.8727 (tt0) REVERT: L 281 CYS cc_start: 0.8894 (t) cc_final: 0.8453 (t) REVERT: 4 53 TRP cc_start: 0.5858 (m100) cc_final: 0.5273 (m100) REVERT: K 38 ILE cc_start: 0.9174 (mt) cc_final: 0.8930 (mt) REVERT: C 229 MET cc_start: 0.9507 (mmp) cc_final: 0.9151 (mmt) REVERT: C 268 LYS cc_start: 0.9530 (tmtm) cc_final: 0.9287 (tttt) REVERT: I 47 CYS cc_start: 0.8799 (t) cc_final: 0.8461 (t) REVERT: G 31 LYS cc_start: 0.8518 (mttt) cc_final: 0.8299 (mttp) REVERT: T 18 LEU cc_start: 0.8950 (tt) cc_final: 0.8740 (tt) REVERT: O 30 VAL cc_start: 0.8906 (p) cc_final: 0.8622 (t) REVERT: V 22 MET cc_start: 0.8943 (mmm) cc_final: 0.8371 (mmm) REVERT: H 15 SER cc_start: 0.9150 (t) cc_final: 0.8808 (p) REVERT: H 38 TRP cc_start: 0.8738 (t60) cc_final: 0.8392 (t60) REVERT: 7 33 SER cc_start: 0.8880 (t) cc_final: 0.8568 (m) REVERT: 1 18 LEU cc_start: 0.8856 (tp) cc_final: 0.7996 (tt) REVERT: 1 22 MET cc_start: 0.9237 (tpt) cc_final: 0.9028 (ptt) REVERT: M 341 GLU cc_start: 0.8899 (pt0) cc_final: 0.8623 (pm20) REVERT: M 391 PHE cc_start: 0.9263 (t80) cc_final: 0.8944 (t80) REVERT: M 414 ASN cc_start: 0.8423 (m-40) cc_final: 0.8082 (t0) REVERT: M 415 LEU cc_start: 0.8802 (tm) cc_final: 0.8326 (tm) REVERT: M 522 ASN cc_start: 0.8953 (t0) cc_final: 0.8639 (t0) REVERT: M 541 MET cc_start: 0.9094 (mmp) cc_final: 0.8357 (mmt) outliers start: 2 outliers final: 2 residues processed: 778 average time/residue: 0.2547 time to fit residues: 327.8465 Evaluate side-chains 551 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 549 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 50.0000 chunk 150 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 0.2980 chunk 155 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 179 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 HIS L 252 ASN 2 44 HIS C 87 GLN C 101 GLN C 176 ASN C 256 GLN C 301 ASN Q 44 HIS M 339 HIS M 446 HIS M 515 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 20936 Z= 0.232 Angle : 1.274 45.319 29503 Z= 0.480 Chirality : 0.044 0.637 3102 Planarity : 0.004 0.065 3485 Dihedral : 19.445 179.937 3898 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.60 % Favored : 85.40 % Rotamer: Outliers : 0.50 % Allowed : 3.89 % Favored : 95.61 % Cbeta Deviations : 0.05 % 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: -2.58 (0.18), residues: 2041 helix: -0.01 (0.14), residues: 1239 sheet: None (None), residues: 0 loop : -4.71 (0.17), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP 8 53 HIS 0.028 0.002 HIS A 27 PHE 0.026 0.002 PHE 9 28 TYR 0.028 0.002 TYR 4 34 ARG 0.006 0.001 ARG L 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 673 time to evaluate : 1.833 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: L 41 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8614 (mp0) REVERT: L 57 VAL cc_start: 0.7337 (OUTLIER) cc_final: 0.6994 (p) REVERT: L 82 LEU cc_start: 0.9502 (tp) cc_final: 0.9200 (tp) REVERT: L 126 PHE cc_start: 0.8981 (t80) cc_final: 0.8761 (t80) REVERT: L 198 ASN cc_start: 0.9118 (m-40) cc_final: 0.8890 (m-40) REVERT: L 228 MET cc_start: 0.8948 (mmm) cc_final: 0.8673 (tpp) REVERT: L 281 CYS cc_start: 0.8903 (t) cc_final: 0.8536 (t) REVERT: 8 53 TRP cc_start: 0.8485 (p90) cc_final: 0.7937 (p90) REVERT: 4 53 TRP cc_start: 0.5371 (m100) cc_final: 0.4483 (m100) REVERT: C 183 GLU cc_start: 0.9070 (pm20) cc_final: 0.8820 (pm20) REVERT: C 201 LEU cc_start: 0.9353 (tp) cc_final: 0.9044 (tp) REVERT: C 205 TYR cc_start: 0.8414 (t80) cc_final: 0.7624 (t80) REVERT: C 261 ILE cc_start: 0.9093 (pt) cc_final: 0.8756 (tt) REVERT: G 27 ASP cc_start: 0.8682 (t70) cc_final: 0.8443 (t0) REVERT: G 31 LYS cc_start: 0.8550 (mttt) cc_final: 0.8107 (mptt) REVERT: Q 47 CYS cc_start: 0.8891 (m) cc_final: 0.8542 (m) REVERT: V 21 VAL cc_start: 0.9389 (p) cc_final: 0.8799 (p) REVERT: V 22 MET cc_start: 0.8876 (mmm) cc_final: 0.8419 (mmm) REVERT: N 25 LEU cc_start: 0.9725 (tt) cc_final: 0.9517 (tt) REVERT: J 33 SER cc_start: 0.8836 (t) cc_final: 0.8605 (t) REVERT: H 15 SER cc_start: 0.9166 (t) cc_final: 0.8794 (p) REVERT: H 38 TRP cc_start: 0.8637 (t60) cc_final: 0.7944 (t60) REVERT: 7 33 SER cc_start: 0.8803 (t) cc_final: 0.8458 (m) REVERT: 1 29 VAL cc_start: 0.9509 (t) cc_final: 0.9309 (p) REVERT: M 341 GLU cc_start: 0.8832 (pt0) cc_final: 0.8601 (pm20) REVERT: M 391 PHE cc_start: 0.9218 (t80) cc_final: 0.8979 (t80) REVERT: M 399 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8020 (ttp80) REVERT: M 415 LEU cc_start: 0.9089 (tp) cc_final: 0.8615 (tp) REVERT: M 522 ASN cc_start: 0.8674 (t0) cc_final: 0.8062 (t0) REVERT: M 526 MET cc_start: 0.8493 (mtp) cc_final: 0.8049 (mtm) REVERT: M 528 SER cc_start: 0.9425 (m) cc_final: 0.8869 (t) REVERT: M 541 MET cc_start: 0.9100 (mmp) cc_final: 0.8454 (mmt) outliers start: 7 outliers final: 1 residues processed: 678 average time/residue: 0.2330 time to fit residues: 266.0650 Evaluate side-chains 527 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 525 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 30.0000 chunk 55 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 191 HIS L 279 ASN C 256 GLN 9 27 HIS ** M 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 20936 Z= 0.338 Angle : 1.285 45.604 29503 Z= 0.489 Chirality : 0.046 0.410 3102 Planarity : 0.005 0.088 3485 Dihedral : 19.167 179.793 3898 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.99 % Favored : 84.96 % Rotamer: Outliers : 0.21 % Allowed : 3.96 % Favored : 95.82 % Cbeta Deviations : 0.00 % 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: -2.17 (0.18), residues: 2041 helix: 0.41 (0.14), residues: 1228 sheet: None (None), residues: 0 loop : -4.63 (0.18), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 53 HIS 0.032 0.003 HIS A 27 PHE 0.031 0.002 PHE T 28 TYR 0.032 0.002 TYR S 34 ARG 0.010 0.001 ARG M 459 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 606 time to evaluate : 1.970 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: L 19 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7704 (tm-30) REVERT: L 41 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8625 (mp0) REVERT: L 82 LEU cc_start: 0.9483 (tp) cc_final: 0.9202 (tp) REVERT: L 86 PHE cc_start: 0.9102 (m-10) cc_final: 0.8897 (m-10) REVERT: L 198 ASN cc_start: 0.9144 (m-40) cc_final: 0.8868 (m-40) REVERT: L 269 TRP cc_start: 0.8349 (m100) cc_final: 0.8098 (m-90) REVERT: L 279 ASN cc_start: 0.8543 (m-40) cc_final: 0.8338 (m110) REVERT: L 281 CYS cc_start: 0.9033 (t) cc_final: 0.8721 (t) REVERT: 8 47 CYS cc_start: 0.9292 (t) cc_final: 0.8956 (t) REVERT: C 199 LEU cc_start: 0.9190 (tp) cc_final: 0.8939 (tt) REVERT: C 205 TYR cc_start: 0.8475 (t80) cc_final: 0.7817 (t80) REVERT: C 261 ILE cc_start: 0.9169 (pt) cc_final: 0.8896 (tt) REVERT: I 47 CYS cc_start: 0.8629 (t) cc_final: 0.8412 (t) REVERT: G 31 LYS cc_start: 0.8610 (mttt) cc_final: 0.8178 (mttm) REVERT: S 53 TRP cc_start: 0.7597 (p-90) cc_final: 0.7259 (p-90) REVERT: V 21 VAL cc_start: 0.9426 (p) cc_final: 0.8955 (p) REVERT: V 22 MET cc_start: 0.8911 (mmm) cc_final: 0.8471 (mmm) REVERT: H 15 SER cc_start: 0.9228 (t) cc_final: 0.8860 (p) REVERT: 7 33 SER cc_start: 0.8895 (t) cc_final: 0.8582 (m) REVERT: 3 22 MET cc_start: 0.9318 (mmm) cc_final: 0.9060 (mmm) REVERT: 1 33 SER cc_start: 0.8837 (m) cc_final: 0.8635 (m) REVERT: M 341 GLU cc_start: 0.8838 (pt0) cc_final: 0.8545 (pm20) REVERT: M 358 VAL cc_start: 0.8353 (t) cc_final: 0.8148 (t) REVERT: M 391 PHE cc_start: 0.9305 (t80) cc_final: 0.8855 (t80) REVERT: M 399 ARG cc_start: 0.8709 (ttp80) cc_final: 0.7946 (ttp80) REVERT: M 522 ASN cc_start: 0.8845 (t0) cc_final: 0.8629 (t0) REVERT: M 526 MET cc_start: 0.8441 (mtp) cc_final: 0.8070 (mtm) REVERT: M 528 SER cc_start: 0.9509 (m) cc_final: 0.9023 (t) REVERT: M 541 MET cc_start: 0.9220 (mmp) cc_final: 0.8495 (mmt) outliers start: 3 outliers final: 0 residues processed: 608 average time/residue: 0.2493 time to fit residues: 260.0994 Evaluate side-chains 507 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 143 GLN L 247 HIS 9 27 HIS ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 637 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20936 Z= 0.216 Angle : 1.179 45.295 29503 Z= 0.443 Chirality : 0.043 0.463 3102 Planarity : 0.004 0.069 3485 Dihedral : 18.569 179.852 3898 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % Rotamer: Outliers : 0.35 % Allowed : 3.89 % Favored : 95.75 % Cbeta Deviations : 0.00 % 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: -1.71 (0.19), residues: 2041 helix: 0.80 (0.15), residues: 1235 sheet: None (None), residues: 0 loop : -4.53 (0.18), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP 8 50 HIS 0.026 0.002 HIS A 27 PHE 0.034 0.001 PHE 5 28 TYR 0.018 0.001 TYR M 480 ARG 0.003 0.001 ARG L 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 606 time to evaluate : 1.942 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: L 41 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8604 (mp0) REVERT: L 82 LEU cc_start: 0.9485 (tp) cc_final: 0.9055 (tp) REVERT: L 198 ASN cc_start: 0.9131 (m-40) cc_final: 0.8906 (m-40) REVERT: 2 42 ILE cc_start: 0.9284 (mm) cc_final: 0.8991 (tp) REVERT: C 199 LEU cc_start: 0.9143 (tp) cc_final: 0.8892 (tt) REVERT: C 205 TYR cc_start: 0.8486 (t80) cc_final: 0.7914 (t80) REVERT: C 261 ILE cc_start: 0.9087 (pt) cc_final: 0.8825 (tt) REVERT: G 31 LYS cc_start: 0.8515 (mttt) cc_final: 0.8096 (mttm) REVERT: S 53 TRP cc_start: 0.7545 (p-90) cc_final: 0.7243 (p-90) REVERT: Q 33 ILE cc_start: 0.9249 (tp) cc_final: 0.9028 (tp) REVERT: V 21 VAL cc_start: 0.9410 (p) cc_final: 0.8951 (p) REVERT: V 22 MET cc_start: 0.8857 (mmm) cc_final: 0.8443 (mmm) REVERT: H 15 SER cc_start: 0.9200 (t) cc_final: 0.8843 (p) REVERT: 9 24 LEU cc_start: 0.9465 (tp) cc_final: 0.8916 (tp) REVERT: 7 33 SER cc_start: 0.8776 (t) cc_final: 0.8444 (m) REVERT: 1 18 LEU cc_start: 0.8914 (tt) cc_final: 0.8252 (tt) REVERT: 1 20 LEU cc_start: 0.9038 (tt) cc_final: 0.8689 (tt) REVERT: 1 22 MET cc_start: 0.9409 (tpt) cc_final: 0.9047 (ptt) REVERT: M 391 PHE cc_start: 0.9271 (t80) cc_final: 0.8621 (t80) REVERT: M 415 LEU cc_start: 0.8969 (tp) cc_final: 0.8545 (tp) REVERT: M 526 MET cc_start: 0.8369 (mtp) cc_final: 0.8134 (mtm) REVERT: M 528 SER cc_start: 0.9460 (m) cc_final: 0.8925 (t) REVERT: M 541 MET cc_start: 0.9024 (mmp) cc_final: 0.8349 (mmt) REVERT: M 605 ILE cc_start: 0.9307 (tp) cc_final: 0.9088 (tp) outliers start: 5 outliers final: 2 residues processed: 609 average time/residue: 0.2300 time to fit residues: 239.5412 Evaluate side-chains 500 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 498 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 143 GLN L 192 HIS C 101 GLN 9 27 HIS ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 20936 Z= 0.221 Angle : 1.154 45.329 29503 Z= 0.438 Chirality : 0.042 0.386 3102 Planarity : 0.004 0.062 3485 Dihedral : 18.354 179.851 3898 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.52 % Favored : 86.48 % Rotamer: Outliers : 0.07 % Allowed : 2.76 % Favored : 97.17 % Cbeta Deviations : 0.00 % 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: -1.60 (0.19), residues: 2041 helix: 0.86 (0.15), residues: 1236 sheet: None (None), residues: 0 loop : -4.44 (0.18), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 53 HIS 0.018 0.002 HIS 5 27 PHE 0.036 0.002 PHE A 28 TYR 0.017 0.001 TYR M 480 ARG 0.008 0.001 ARG M 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 592 time to evaluate : 1.903 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: 0 27 ASP cc_start: 0.8554 (t70) cc_final: 0.8310 (t0) REVERT: L 41 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8632 (mp0) REVERT: L 57 VAL cc_start: 0.7510 (t) cc_final: 0.7289 (p) REVERT: L 198 ASN cc_start: 0.9153 (m-40) cc_final: 0.8901 (m-40) REVERT: L 269 TRP cc_start: 0.8262 (m100) cc_final: 0.8003 (m-90) REVERT: L 281 CYS cc_start: 0.8940 (t) cc_final: 0.8673 (t) REVERT: L 285 SER cc_start: 0.9099 (m) cc_final: 0.8860 (m) REVERT: 2 42 ILE cc_start: 0.9240 (mm) cc_final: 0.8962 (tp) REVERT: C 199 LEU cc_start: 0.9158 (tp) cc_final: 0.8838 (tt) REVERT: C 205 TYR cc_start: 0.8537 (t80) cc_final: 0.7965 (t80) REVERT: C 261 ILE cc_start: 0.9104 (pt) cc_final: 0.8843 (tt) REVERT: G 31 LYS cc_start: 0.8511 (mttt) cc_final: 0.8093 (mttm) REVERT: S 53 TRP cc_start: 0.7542 (p-90) cc_final: 0.7263 (p-90) REVERT: H 15 SER cc_start: 0.9189 (t) cc_final: 0.8845 (p) REVERT: H 22 MET cc_start: 0.8886 (mmm) cc_final: 0.8672 (tpt) REVERT: A 31 LEU cc_start: 0.8757 (tt) cc_final: 0.8078 (mp) REVERT: 9 24 LEU cc_start: 0.9284 (tp) cc_final: 0.8930 (tp) REVERT: 7 33 SER cc_start: 0.8793 (t) cc_final: 0.8443 (m) REVERT: 1 18 LEU cc_start: 0.8926 (tt) cc_final: 0.8249 (tt) REVERT: 1 22 MET cc_start: 0.9405 (tpt) cc_final: 0.9005 (ptt) REVERT: 1 33 SER cc_start: 0.8659 (m) cc_final: 0.8385 (m) REVERT: M 391 PHE cc_start: 0.9241 (t80) cc_final: 0.8641 (t80) REVERT: M 528 SER cc_start: 0.9402 (m) cc_final: 0.8857 (t) REVERT: M 541 MET cc_start: 0.9047 (mmp) cc_final: 0.8433 (mmt) REVERT: M 605 ILE cc_start: 0.9275 (tp) cc_final: 0.9064 (tp) outliers start: 1 outliers final: 1 residues processed: 593 average time/residue: 0.2211 time to fit residues: 224.7354 Evaluate side-chains 492 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 491 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 0.0040 chunk 15 optimal weight: 10.0000 chunk 63 optimal weight: 0.0030 chunk 100 optimal weight: 7.9990 overall best weight: 1.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 143 GLN ** L 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 HIS ** L 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 44 HIS ** C 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 637 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20936 Z= 0.189 Angle : 1.135 45.233 29503 Z= 0.429 Chirality : 0.042 0.332 3102 Planarity : 0.004 0.069 3485 Dihedral : 17.951 179.844 3898 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Cbeta Deviations : 0.00 % 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: -1.47 (0.19), residues: 2041 helix: 0.97 (0.15), residues: 1234 sheet: None (None), residues: 0 loop : -4.38 (0.18), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP H 38 HIS 0.033 0.002 HIS A 27 PHE 0.030 0.001 PHE M 531 TYR 0.043 0.001 TYR I 34 ARG 0.007 0.001 ARG M 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 591 time to evaluate : 2.038 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: 0 27 ASP cc_start: 0.8510 (t70) cc_final: 0.8254 (t0) REVERT: L 41 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8623 (mp0) REVERT: L 86 PHE cc_start: 0.9095 (m-80) cc_final: 0.8690 (m-80) REVERT: L 198 ASN cc_start: 0.9170 (m-40) cc_final: 0.8898 (m-40) REVERT: L 269 TRP cc_start: 0.8141 (m100) cc_final: 0.7935 (m-90) REVERT: L 285 SER cc_start: 0.9015 (m) cc_final: 0.8780 (m) REVERT: 2 42 ILE cc_start: 0.9228 (mm) cc_final: 0.9016 (tp) REVERT: C 199 LEU cc_start: 0.9104 (tp) cc_final: 0.8790 (tt) REVERT: C 205 TYR cc_start: 0.8530 (t80) cc_final: 0.7984 (t80) REVERT: C 261 ILE cc_start: 0.9058 (pt) cc_final: 0.8816 (tt) REVERT: I 30 VAL cc_start: 0.8624 (p) cc_final: 0.8371 (m) REVERT: G 31 LYS cc_start: 0.8476 (mttt) cc_final: 0.8070 (mttm) REVERT: S 53 TRP cc_start: 0.7522 (p-90) cc_final: 0.7256 (p-90) REVERT: H 15 SER cc_start: 0.9192 (t) cc_final: 0.8875 (p) REVERT: A 31 LEU cc_start: 0.8700 (tt) cc_final: 0.8162 (mp) REVERT: 7 33 SER cc_start: 0.8735 (t) cc_final: 0.8378 (m) REVERT: 1 18 LEU cc_start: 0.8875 (tt) cc_final: 0.8120 (tt) REVERT: 1 22 MET cc_start: 0.9345 (tpt) cc_final: 0.8930 (ptt) REVERT: M 343 TYR cc_start: 0.7095 (m-80) cc_final: 0.6707 (m-80) REVERT: M 391 PHE cc_start: 0.9152 (t80) cc_final: 0.8827 (t80) REVERT: M 415 LEU cc_start: 0.8908 (tp) cc_final: 0.8564 (tp) REVERT: M 528 SER cc_start: 0.9403 (m) cc_final: 0.8828 (t) REVERT: M 541 MET cc_start: 0.9159 (mmp) cc_final: 0.8580 (mmt) REVERT: M 605 ILE cc_start: 0.9286 (tp) cc_final: 0.9061 (tp) outliers start: 2 outliers final: 2 residues processed: 591 average time/residue: 0.2548 time to fit residues: 260.0417 Evaluate side-chains 504 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 502 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 161 optimal weight: 0.0040 chunk 106 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 overall best weight: 3.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 637 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 20936 Z= 0.255 Angle : 1.148 45.405 29503 Z= 0.437 Chirality : 0.043 0.358 3102 Planarity : 0.004 0.064 3485 Dihedral : 17.932 179.887 3898 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % 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: -1.56 (0.19), residues: 2041 helix: 0.88 (0.15), residues: 1234 sheet: None (None), residues: 0 loop : -4.39 (0.18), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 8 50 HIS 0.025 0.002 HIS 3 27 PHE 0.024 0.002 PHE M 531 TYR 0.015 0.002 TYR M 480 ARG 0.006 0.001 ARG M 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 584 time to evaluate : 1.797 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: 0 27 ASP cc_start: 0.8493 (t70) cc_final: 0.8236 (t0) REVERT: L 41 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8633 (mp0) REVERT: L 86 PHE cc_start: 0.9074 (m-80) cc_final: 0.8542 (m-80) REVERT: L 198 ASN cc_start: 0.9200 (m-40) cc_final: 0.8945 (m-40) REVERT: L 269 TRP cc_start: 0.8186 (m100) cc_final: 0.7854 (m-90) REVERT: L 279 ASN cc_start: 0.8092 (m-40) cc_final: 0.7789 (m110) REVERT: L 285 SER cc_start: 0.9058 (m) cc_final: 0.8811 (m) REVERT: C 199 LEU cc_start: 0.9151 (tp) cc_final: 0.8887 (tt) REVERT: C 205 TYR cc_start: 0.8553 (t80) cc_final: 0.7996 (t80) REVERT: C 261 ILE cc_start: 0.9092 (pt) cc_final: 0.8877 (tt) REVERT: G 31 LYS cc_start: 0.8493 (mttt) cc_final: 0.8209 (mttm) REVERT: T 22 MET cc_start: 0.8833 (tpp) cc_final: 0.8572 (tmm) REVERT: T 26 ILE cc_start: 0.9352 (mt) cc_final: 0.8681 (mt) REVERT: V 22 MET cc_start: 0.8725 (ttp) cc_final: 0.8446 (tmm) REVERT: H 15 SER cc_start: 0.9200 (t) cc_final: 0.8884 (p) REVERT: A 31 LEU cc_start: 0.8799 (tt) cc_final: 0.8144 (mp) REVERT: 9 24 LEU cc_start: 0.9219 (tp) cc_final: 0.8990 (tp) REVERT: 7 33 SER cc_start: 0.8842 (t) cc_final: 0.8497 (m) REVERT: 3 32 SER cc_start: 0.8750 (t) cc_final: 0.8345 (p) REVERT: 1 18 LEU cc_start: 0.8869 (tt) cc_final: 0.8104 (tt) REVERT: 1 22 MET cc_start: 0.9392 (tpt) cc_final: 0.8984 (ptt) REVERT: M 343 TYR cc_start: 0.7093 (m-80) cc_final: 0.6645 (m-80) REVERT: M 391 PHE cc_start: 0.9220 (t80) cc_final: 0.8656 (t80) REVERT: M 507 ASP cc_start: 0.8887 (t0) cc_final: 0.8589 (t0) REVERT: M 528 SER cc_start: 0.9451 (m) cc_final: 0.8896 (t) REVERT: M 541 MET cc_start: 0.9217 (mmp) cc_final: 0.8665 (mmt) REVERT: M 605 ILE cc_start: 0.9263 (tp) cc_final: 0.9048 (tp) outliers start: 0 outliers final: 0 residues processed: 584 average time/residue: 0.2243 time to fit residues: 224.5232 Evaluate side-chains 491 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 491 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.0980 chunk 76 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 121 optimal weight: 0.0470 chunk 130 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 overall best weight: 3.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 HIS 4 44 HIS C 101 GLN 9 27 HIS ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 637 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 20936 Z= 0.222 Angle : 1.128 45.293 29503 Z= 0.430 Chirality : 0.042 0.359 3102 Planarity : 0.004 0.073 3485 Dihedral : 17.656 179.847 3898 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 0.14 % Allowed : 1.63 % Favored : 98.23 % Cbeta Deviations : 0.00 % 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: -1.46 (0.19), residues: 2041 helix: 0.96 (0.15), residues: 1229 sheet: None (None), residues: 0 loop : -4.31 (0.18), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 53 HIS 0.023 0.002 HIS 3 27 PHE 0.023 0.002 PHE M 531 TYR 0.041 0.002 TYR I 34 ARG 0.006 0.001 ARG M 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 581 time to evaluate : 2.048 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: 0 27 ASP cc_start: 0.8449 (t70) cc_final: 0.8183 (t0) REVERT: L 41 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8605 (mp0) REVERT: L 86 PHE cc_start: 0.9092 (m-80) cc_final: 0.8511 (m-80) REVERT: L 126 PHE cc_start: 0.9215 (t80) cc_final: 0.8782 (t80) REVERT: L 198 ASN cc_start: 0.9157 (m-40) cc_final: 0.8950 (m-40) REVERT: L 269 TRP cc_start: 0.8216 (m100) cc_final: 0.7887 (m-90) REVERT: L 285 SER cc_start: 0.9045 (m) cc_final: 0.8791 (m) REVERT: C 199 LEU cc_start: 0.9150 (tp) cc_final: 0.8815 (tt) REVERT: C 205 TYR cc_start: 0.8517 (t80) cc_final: 0.7953 (t80) REVERT: C 261 ILE cc_start: 0.9072 (pt) cc_final: 0.8856 (tt) REVERT: G 31 LYS cc_start: 0.8361 (mttt) cc_final: 0.7881 (mptt) REVERT: V 22 MET cc_start: 0.8652 (ttp) cc_final: 0.8367 (tmm) REVERT: H 15 SER cc_start: 0.9172 (t) cc_final: 0.8904 (p) REVERT: A 31 LEU cc_start: 0.8730 (tt) cc_final: 0.8126 (mp) REVERT: 7 33 SER cc_start: 0.8800 (t) cc_final: 0.8423 (m) REVERT: 1 18 LEU cc_start: 0.8847 (tt) cc_final: 0.8049 (tt) REVERT: 1 22 MET cc_start: 0.9424 (tpt) cc_final: 0.9017 (ptt) REVERT: M 343 TYR cc_start: 0.7079 (m-80) cc_final: 0.6575 (m-80) REVERT: M 391 PHE cc_start: 0.9206 (t80) cc_final: 0.8638 (t80) REVERT: M 415 LEU cc_start: 0.8882 (tp) cc_final: 0.8516 (tp) REVERT: M 507 ASP cc_start: 0.8805 (t0) cc_final: 0.8483 (t0) REVERT: M 528 SER cc_start: 0.9455 (m) cc_final: 0.8924 (t) REVERT: M 541 MET cc_start: 0.9196 (mmp) cc_final: 0.8642 (mmt) REVERT: M 605 ILE cc_start: 0.9224 (tp) cc_final: 0.9003 (tp) outliers start: 2 outliers final: 1 residues processed: 582 average time/residue: 0.2310 time to fit residues: 230.2564 Evaluate side-chains 490 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 489 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 166 optimal weight: 50.0000 chunk 177 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 54 optimal weight: 40.0000 chunk 160 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 192 HIS ** L 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 20936 Z= 0.275 Angle : 1.155 45.418 29503 Z= 0.445 Chirality : 0.043 0.380 3102 Planarity : 0.004 0.068 3485 Dihedral : 17.719 179.843 3898 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % 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: -1.52 (0.19), residues: 2041 helix: 0.92 (0.15), residues: 1226 sheet: None (None), residues: 0 loop : -4.34 (0.18), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP H 38 HIS 0.026 0.002 HIS 1 27 PHE 0.031 0.002 PHE L 207 TYR 0.016 0.002 TYR C 62 ARG 0.005 0.001 ARG M 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 582 time to evaluate : 1.813 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: 0 27 ASP cc_start: 0.8446 (t70) cc_final: 0.8187 (t0) REVERT: L 126 PHE cc_start: 0.9183 (t80) cc_final: 0.8690 (t80) REVERT: L 205 ASN cc_start: 0.8538 (p0) cc_final: 0.8272 (p0) REVERT: L 269 TRP cc_start: 0.8311 (m100) cc_final: 0.7936 (m-90) REVERT: L 285 SER cc_start: 0.9081 (m) cc_final: 0.8827 (m) REVERT: 2 42 ILE cc_start: 0.9295 (mm) cc_final: 0.9038 (tp) REVERT: C 147 LEU cc_start: 0.9340 (tt) cc_final: 0.9060 (tt) REVERT: C 199 LEU cc_start: 0.9174 (tp) cc_final: 0.8860 (tt) REVERT: C 205 TYR cc_start: 0.8559 (t80) cc_final: 0.8008 (t80) REVERT: G 31 LYS cc_start: 0.8431 (mttt) cc_final: 0.7946 (mptt) REVERT: T 22 MET cc_start: 0.8815 (tpp) cc_final: 0.8493 (tmm) REVERT: T 26 ILE cc_start: 0.9347 (mt) cc_final: 0.8662 (mt) REVERT: T 31 LEU cc_start: 0.9270 (tt) cc_final: 0.8865 (mm) REVERT: H 15 SER cc_start: 0.9190 (t) cc_final: 0.8903 (p) REVERT: H 38 TRP cc_start: 0.8252 (t60) cc_final: 0.7481 (t60) REVERT: A 31 LEU cc_start: 0.8797 (tt) cc_final: 0.8110 (mp) REVERT: 7 33 SER cc_start: 0.8903 (t) cc_final: 0.8463 (m) REVERT: 3 32 SER cc_start: 0.8965 (t) cc_final: 0.8560 (p) REVERT: 1 18 LEU cc_start: 0.8771 (tt) cc_final: 0.7970 (tt) REVERT: 1 22 MET cc_start: 0.9425 (tpt) cc_final: 0.9014 (ptt) REVERT: M 400 GLN cc_start: 0.8642 (mp10) cc_final: 0.8316 (mp10) REVERT: M 507 ASP cc_start: 0.8866 (t0) cc_final: 0.8536 (t0) REVERT: M 528 SER cc_start: 0.9446 (m) cc_final: 0.8964 (t) REVERT: M 541 MET cc_start: 0.9220 (mmp) cc_final: 0.8780 (mmt) REVERT: M 605 ILE cc_start: 0.9263 (tp) cc_final: 0.9044 (tp) outliers start: 0 outliers final: 0 residues processed: 582 average time/residue: 0.2337 time to fit residues: 232.6909 Evaluate side-chains 489 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 HIS C 101 GLN 9 27 HIS ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 518 ASN M 637 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 20936 Z= 0.280 Angle : 1.151 45.381 29503 Z= 0.446 Chirality : 0.044 0.375 3102 Planarity : 0.004 0.075 3485 Dihedral : 17.562 179.867 3898 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % Rotamer: Outliers : 0.14 % Allowed : 0.92 % Favored : 98.94 % Cbeta Deviations : 0.00 % 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: -1.61 (0.19), residues: 2041 helix: 0.82 (0.15), residues: 1229 sheet: None (None), residues: 0 loop : -4.34 (0.18), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP H 38 HIS 0.050 0.003 HIS A 27 PHE 0.038 0.002 PHE 5 28 TYR 0.034 0.002 TYR I 34 ARG 0.006 0.001 ARG M 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 578 time to evaluate : 1.937 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: 0 27 ASP cc_start: 0.8443 (t70) cc_final: 0.8185 (t0) REVERT: L 41 GLU cc_start: 0.8797 (mp0) cc_final: 0.8524 (mp0) REVERT: L 126 PHE cc_start: 0.9183 (t80) cc_final: 0.8674 (t80) REVERT: L 205 ASN cc_start: 0.8506 (p0) cc_final: 0.8237 (p0) REVERT: L 269 TRP cc_start: 0.8307 (m100) cc_final: 0.7920 (m-90) REVERT: L 279 ASN cc_start: 0.8773 (m-40) cc_final: 0.8565 (m110) REVERT: 2 42 ILE cc_start: 0.9297 (mm) cc_final: 0.9035 (tp) REVERT: C 146 MET cc_start: 0.8553 (tmm) cc_final: 0.8314 (ttm) REVERT: C 199 LEU cc_start: 0.9200 (tp) cc_final: 0.8870 (tt) REVERT: C 205 TYR cc_start: 0.8619 (t80) cc_final: 0.8074 (t80) REVERT: G 31 LYS cc_start: 0.8439 (mttt) cc_final: 0.7897 (mptt) REVERT: T 22 MET cc_start: 0.8827 (tpp) cc_final: 0.8506 (tmm) REVERT: T 26 ILE cc_start: 0.9350 (mt) cc_final: 0.8624 (mt) REVERT: T 31 LEU cc_start: 0.9285 (tt) cc_final: 0.8870 (mm) REVERT: H 15 SER cc_start: 0.9238 (t) cc_final: 0.8955 (p) REVERT: A 31 LEU cc_start: 0.8815 (tt) cc_final: 0.8121 (mp) REVERT: 7 33 SER cc_start: 0.8923 (t) cc_final: 0.8478 (m) REVERT: 1 18 LEU cc_start: 0.8767 (tt) cc_final: 0.7962 (tt) REVERT: 1 22 MET cc_start: 0.9431 (tpt) cc_final: 0.9016 (ptt) REVERT: M 400 GLN cc_start: 0.8542 (mp10) cc_final: 0.8322 (mp10) REVERT: M 415 LEU cc_start: 0.8871 (tp) cc_final: 0.8562 (tp) REVERT: M 507 ASP cc_start: 0.8888 (t0) cc_final: 0.8520 (t0) REVERT: M 528 SER cc_start: 0.9475 (m) cc_final: 0.8960 (t) REVERT: M 541 MET cc_start: 0.9327 (mmp) cc_final: 0.8699 (mmt) REVERT: M 605 ILE cc_start: 0.9263 (tp) cc_final: 0.9046 (tp) outliers start: 2 outliers final: 1 residues processed: 580 average time/residue: 0.2573 time to fit residues: 257.3719 Evaluate side-chains 492 residues out of total 1780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 491 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 50.0000 chunk 48 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 192 HIS L 247 HIS C 101 GLN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 27 HIS ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 637 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.102870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.091133 restraints weight = 64985.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093318 restraints weight = 30471.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.094657 restraints weight = 17554.437| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 20936 Z= 0.257 Angle : 1.140 45.345 29503 Z= 0.441 Chirality : 0.043 0.372 3102 Planarity : 0.004 0.071 3485 Dihedral : 17.364 179.867 3898 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % 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: -1.53 (0.19), residues: 2041 helix: 0.90 (0.15), residues: 1228 sheet: None (None), residues: 0 loop : -4.32 (0.18), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP H 38 HIS 0.041 0.002 HIS A 27 PHE 0.040 0.002 PHE 5 28 TYR 0.015 0.002 TYR C 62 ARG 0.005 0.001 ARG M 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4472.75 seconds wall clock time: 81 minutes 18.21 seconds (4878.21 seconds total)