Starting phenix.real_space_refine (version: dev) on Mon Feb 27 10:22:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxf_33501/02_2023/7xxf_33501_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxf_33501/02_2023/7xxf_33501.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxf_33501/02_2023/7xxf_33501_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxf_33501/02_2023/7xxf_33501_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxf_33501/02_2023/7xxf_33501_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxf_33501/02_2023/7xxf_33501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxf_33501/02_2023/7xxf_33501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxf_33501/02_2023/7xxf_33501_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxf_33501/02_2023/7xxf_33501_updated.pdb" } resolution = 2.24 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 29826 Number of models: 1 Model: "" Number of chains: 120 Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2655 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 316} Chain: "L" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2177 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 258} Chain: "M" Number of atoms: 2550 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2543 Classifications: {'peptide': 320} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 300} Conformer: "B" Number of residues, atoms: 320, 2543 Classifications: {'peptide': 320} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 300} bond proxies already assigned to first conformer: 2637 Chain: "H" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2000 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 233} Chain: "A" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "F" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "I" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 394 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "K" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "N" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "O" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 389 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Q" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 389 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "S" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 475 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "U" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 443 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "W" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 470 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Y" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "Z" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "1" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 395 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "2" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "3" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 472 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 51} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "5" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 389 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "7" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 389 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "9" Number of atoms: 392 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 388 Chain: "0" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "a" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 296 Unusual residues: {'HEC': 4, 'PGV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 539 Unusual residues: {'BCL': 2, 'BPH': 1, 'LMT': 2, 'PGV': 5, 'U10': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 150 Planarities with less than four sites: {'PGV:plan-3': 5, 'U10:plan-2': 1, 'U10:plan-8': 3, 'U10:plan-9': 3, 'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 3, 'U10:plan-7': 3, 'U10:plan-10': 3, 'U10:plan-11': 3} Unresolved non-hydrogen planarities: 101 Chain: "M" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 514 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CDL': 2, 'I7D': 1, 'MQ9': 1, 'PEE': 1, 'PGV': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 134 Planarities with less than four sites: {'CDL:plan-4': 1, 'PGV:plan-3': 1, 'MQ9:plan-3': 1, 'MQ9:plan-6': 1, 'MQ9:plan-5': 1, 'MQ9:plan-4': 1} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'CDL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 169 Unusual residues: {'BCL': 1, 'CDL': 1, 'I7D': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'BCL': 1, 'I7D': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'BCL': 1, 'I7D': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'I7D': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 183 Unusual residues: {'BCL': 1, 'CDL': 1, 'I7D': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "U" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 146 Unusual residues: {'BCL': 1, 'I7D': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "3" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 142 Unusual residues: {'BCL': 1, 'I7D': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "4" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 177 Unusual residues: {'BCL': 1, 'PGV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 6 Chain: "6" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 243 Unusual residues: {'BCL': 1, 'CDL': 2, 'I7D': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 68 Chain: "7" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 129 Unusual residues: {'BCL': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "8" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 129 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "C" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 136 Classifications: {'water': 136} Link IDs: {None: 135} Chain: "L" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "M" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "H" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "Q" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "S" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "U" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "V" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "W" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "X" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "Z" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "3" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "4" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "7" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "8" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AVAL M 58 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL M 58 " occ=0.50 residue: pdb=" N ALEU 9 6 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU 9 6 " occ=0.50 Time building chain proxies: 18.78, per 1000 atoms: 0.63 Number of scatterers: 29826 At special positions: 0 Unit cell: (133.66, 133.66, 142.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 116 16.00 P 37 15.00 Mg 36 11.99 O 5122 8.00 N 4137 7.00 C 20373 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS M 170 " - pdb=" SG CYS M 172 " distance=2.04 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=48, symmetry=0 Number of additional bonds: simple=48, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.82 Conformation dependent library (CDL) restraints added in 4.3 seconds 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5570 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 5 sheets defined 58.8% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'C' and resid 3 through 26 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 76 through 79 No H-bonds generated for 'chain 'C' and resid 76 through 79' Processing helix chain 'C' and resid 91 through 105 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 126 through 144 Processing helix chain 'C' and resid 146 through 149 No H-bonds generated for 'chain 'C' and resid 146 through 149' Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 235 through 252 removed outlier: 3.914A pdb=" N TRP C 240 " --> pdb=" O LYS C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 258 No H-bonds generated for 'chain 'C' and resid 256 through 258' Processing helix chain 'C' and resid 273 through 291 removed outlier: 3.663A pdb=" N ARG C 283 " --> pdb=" O TRP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 297 Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 326 through 329 Processing helix chain 'C' and resid 337 through 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' Processing helix chain 'L' and resid 7 through 10 Processing helix chain 'L' and resid 20 through 22 No H-bonds generated for 'chain 'L' and resid 20 through 22' Processing helix chain 'L' and resid 33 through 56 Processing helix chain 'L' and resid 72 through 74 No H-bonds generated for 'chain 'L' and resid 72 through 74' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 85 through 111 Processing helix chain 'L' and resid 117 through 133 removed outlier: 3.820A pdb=" N PHE L 124 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 140 Processing helix chain 'L' and resid 143 through 145 No H-bonds generated for 'chain 'L' and resid 143 through 145' Processing helix chain 'L' and resid 153 through 164 Processing helix chain 'L' and resid 168 through 170 No H-bonds generated for 'chain 'L' and resid 168 through 170' Processing helix chain 'L' and resid 172 through 199 Processing helix chain 'L' and resid 210 through 221 removed outlier: 3.832A pdb=" N PHE L 217 " --> pdb=" O GLU L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 254 removed outlier: 3.529A pdb=" N HIS L 231 " --> pdb=" O THR L 227 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER L 252 " --> pdb=" O CYS L 248 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY L 253 " --> pdb=" O ILE L 249 " (cutoff:3.500A) Proline residue: L 254 - end of helix Processing helix chain 'L' and resid 260 through 268 removed outlier: 4.077A pdb=" N TRP L 264 " --> pdb=" O TRP L 260 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER L 265 " --> pdb=" O PRO L 261 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TRP L 266 " --> pdb=" O GLU L 262 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 43 removed outlier: 4.225A pdb=" N ILE M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 78 Processing helix chain 'M' and resid 83 through 92 removed outlier: 5.633A pdb=" N PHE M 91 " --> pdb=" O PHE M 87 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TRP M 92 " --> pdb=" O ARG M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 109 through 111 No H-bonds generated for 'chain 'M' and resid 109 through 111' Processing helix chain 'M' and resid 113 through 139 Processing helix chain 'M' and resid 145 through 161 Processing helix chain 'M' and resid 163 through 168 Processing helix chain 'M' and resid 171 through 173 No H-bonds generated for 'chain 'M' and resid 171 through 173' Processing helix chain 'M' and resid 179 through 192 Processing helix chain 'M' and resid 196 through 198 No H-bonds generated for 'chain 'M' and resid 196 through 198' Processing helix chain 'M' and resid 200 through 229 removed outlier: 4.957A pdb=" N ARG M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PHE M 229 " --> pdb=" O ALA M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 256 Processing helix chain 'M' and resid 264 through 286 removed outlier: 4.039A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 300 Processing helix chain 'M' and resid 317 through 320 No H-bonds generated for 'chain 'M' and resid 317 through 320' Processing helix chain 'H' and resid 12 through 37 removed outlier: 4.091A pdb=" N ARG H 37 " --> pdb=" O MET H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 68 No H-bonds generated for 'chain 'H' and resid 66 through 68' Processing helix chain 'H' and resid 105 through 107 No H-bonds generated for 'chain 'H' and resid 105 through 107' Processing helix chain 'H' and resid 111 through 113 No H-bonds generated for 'chain 'H' and resid 111 through 113' Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'H' and resid 215 through 220 removed outlier: 3.903A pdb=" N LEU H 219 " --> pdb=" O GLY H 215 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU H 220 " --> pdb=" O GLU H 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 215 through 220' Processing helix chain 'H' and resid 232 through 248 removed outlier: 3.817A pdb=" N GLY H 245 " --> pdb=" O TYR H 241 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N HIS H 246 " --> pdb=" O PHE H 242 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU H 247 " --> pdb=" O ALA H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 254 No H-bonds generated for 'chain 'H' and resid 251 through 254' Processing helix chain 'A' and resid 3 through 6 Processing helix chain 'A' and resid 10 through 34 Processing helix chain 'B' and resid 13 through 44 Processing helix chain 'D' and resid 3 through 6 Processing helix chain 'D' and resid 10 through 34 Processing helix chain 'E' and resid 13 through 44 Processing helix chain 'F' and resid 3 through 6 Processing helix chain 'F' and resid 10 through 34 Processing helix chain 'G' and resid 13 through 44 Processing helix chain 'I' and resid 3 through 6 Processing helix chain 'I' and resid 10 through 34 Processing helix chain 'J' and resid 13 through 44 Processing helix chain 'K' and resid 3 through 6 Processing helix chain 'K' and resid 10 through 34 Processing helix chain 'N' and resid 13 through 44 Processing helix chain 'O' and resid 3 through 7 Processing helix chain 'O' and resid 10 through 33 Processing helix chain 'P' and resid 13 through 44 Processing helix chain 'Q' and resid 3 through 7 removed outlier: 3.846A pdb=" N LEU Q 7 " --> pdb=" O MET Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 33 Processing helix chain 'R' and resid 13 through 44 Processing helix chain 'S' and resid 3 through 6 Processing helix chain 'S' and resid 10 through 33 Processing helix chain 'T' and resid 13 through 44 removed outlier: 3.564A pdb=" N PHE T 19 " --> pdb=" O GLU T 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 34 Processing helix chain 'V' and resid 13 through 44 removed outlier: 3.714A pdb=" N LYS V 17 " --> pdb=" O GLU V 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 7 Processing helix chain 'W' and resid 10 through 34 Processing helix chain 'X' and resid 13 through 44 Processing helix chain 'Y' and resid 3 through 6 Processing helix chain 'Y' and resid 10 through 34 Processing helix chain 'Z' and resid 13 through 44 removed outlier: 3.811A pdb=" N THR Z 25 " --> pdb=" O GLY Z 21 " (cutoff:3.500A) Processing helix chain '1' and resid 3 through 6 Processing helix chain '1' and resid 10 through 34 Processing helix chain '2' and resid 13 through 44 removed outlier: 3.613A pdb=" N LYS 2 17 " --> pdb=" O GLU 2 13 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 6 Processing helix chain '3' and resid 10 through 33 Processing helix chain '4' and resid 13 through 44 Processing helix chain '5' and resid 3 through 6 Processing helix chain '5' and resid 10 through 33 Processing helix chain '6' and resid 13 through 44 Processing helix chain '7' and resid 3 through 7 Processing helix chain '7' and resid 10 through 12 No H-bonds generated for 'chain '7' and resid 10 through 12' Processing helix chain '7' and resid 14 through 34 Processing helix chain '8' and resid 13 through 44 Processing helix chain '9' and resid 10 through 33 Processing helix chain '0' and resid 13 through 44 Processing helix chain 'a' and resid 3 through 20 Proline residue: a 12 - end of helix Processing helix chain 'b' and resid 3 through 21 Proline residue: b 12 - end of helix Processing helix chain 'c' and resid 3 through 19 removed outlier: 3.628A pdb=" N ILE c 8 " --> pdb=" O VAL c 4 " (cutoff:3.500A) Proline residue: c 12 - end of helix Processing helix chain 'd' and resid 3 through 20 removed outlier: 3.720A pdb=" N ILE d 8 " --> pdb=" O VAL d 4 " (cutoff:3.500A) Proline residue: d 12 - end of helix Processing helix chain 'e' and resid 3 through 18 Proline residue: e 12 - end of helix Processing helix chain 'f' and resid 3 through 21 Proline residue: f 12 - end of helix Processing helix chain 'g' and resid 3 through 21 removed outlier: 3.518A pdb=" N ILE g 8 " --> pdb=" O VAL g 4 " (cutoff:3.500A) Proline residue: g 12 - end of helix Processing helix chain 'h' and resid 3 through 20 removed outlier: 3.705A pdb=" N ILE h 8 " --> pdb=" O VAL h 4 " (cutoff:3.500A) Proline residue: h 12 - end of helix Processing helix chain 'i' and resid 3 through 21 removed outlier: 3.514A pdb=" N ILE i 8 " --> pdb=" O VAL i 4 " (cutoff:3.500A) Proline residue: i 12 - end of helix removed outlier: 3.894A pdb=" N ARG i 21 " --> pdb=" O VAL i 17 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 20 removed outlier: 3.632A pdb=" N ILE j 8 " --> pdb=" O VAL j 4 " (cutoff:3.500A) Proline residue: j 12 - end of helix Processing helix chain 'k' and resid 3 through 21 removed outlier: 3.827A pdb=" N ILE k 8 " --> pdb=" O VAL k 4 " (cutoff:3.500A) Proline residue: k 12 - end of helix removed outlier: 3.584A pdb=" N VAL k 17 " --> pdb=" O ALA k 13 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 32 through 36 Processing sheet with id= B, first strand: chain 'H' and resid 61 through 64 Processing sheet with id= C, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= D, first strand: chain 'H' and resid 133 through 135 removed outlier: 6.778A pdb=" N GLU H 183 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA H 170 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR H 181 " --> pdb=" O ALA H 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 200 through 202 removed outlier: 6.435A pdb=" N ASP H 155 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY H 165 " --> pdb=" O LEU H 156 " (cutoff:3.500A) 1290 hydrogen bonds defined for protein. 3796 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: 8.67 Time building geometry restraints manager: 15.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 10270 1.38 - 1.56: 19664 1.56 - 1.74: 74 1.74 - 1.93: 222 1.93 - 2.11: 156 Bond restraints: 30386 Sorted by residual: bond pdb=" CA7 CDL H 303 " pdb=" OA8 CDL H 303 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.22e+02 bond pdb=" CA7 CDL A 101 " pdb=" OA8 CDL A 101 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" CA7 CDL 0 101 " pdb=" OA8 CDL 0 101 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CA7 CDL 6 101 " pdb=" OA8 CDL 6 101 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.18e+02 bond pdb=" CA7 CDL 6 104 " pdb=" OA8 CDL 6 104 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.17e+02 ... (remaining 30381 not shown) Histogram of bond angle deviations from ideal: 82.94 - 102.23: 495 102.23 - 121.51: 33838 121.51 - 140.79: 7284 140.79 - 160.08: 38 160.08 - 179.36: 80 Bond angle restraints: 41735 Sorted by residual: angle pdb=" C25 I7D 8 101 " pdb=" C26 I7D 8 101 " pdb=" C27 I7D 8 101 " ideal model delta sigma weight residual 85.88 131.88 -46.00 3.00e+00 1.11e-01 2.35e+02 angle pdb=" C11 I7D E 101 " pdb=" C12 I7D E 101 " pdb=" C13 I7D E 101 " ideal model delta sigma weight residual 74.50 118.92 -44.42 3.00e+00 1.11e-01 2.19e+02 angle pdb=" C11 I7D 4 101 " pdb=" C12 I7D 4 101 " pdb=" C13 I7D 4 101 " ideal model delta sigma weight residual 74.50 118.90 -44.40 3.00e+00 1.11e-01 2.19e+02 angle pdb=" C11 I7D N 101 " pdb=" C12 I7D N 101 " pdb=" C13 I7D N 101 " ideal model delta sigma weight residual 74.50 118.86 -44.36 3.00e+00 1.11e-01 2.19e+02 angle pdb=" C11 I7D 3 101 " pdb=" C12 I7D 3 101 " pdb=" C13 I7D 3 101 " ideal model delta sigma weight residual 74.50 118.81 -44.31 3.00e+00 1.11e-01 2.18e+02 ... (remaining 41730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 15338 35.52 - 71.04: 576 71.04 - 106.56: 70 106.56 - 142.08: 44 142.08 - 177.60: 48 Dihedral angle restraints: 16076 sinusoidal: 7491 harmonic: 8585 Sorted by residual: dihedral pdb=" C1 BCL Z 101 " pdb=" CGA BCL Z 101 " pdb=" O2A BCL Z 101 " pdb=" CBA BCL Z 101 " ideal model delta sinusoidal sigma weight residual 180.00 131.90 48.10 1 6.00e+00 2.78e-02 8.86e+01 dihedral pdb=" C1 BCL X 102 " pdb=" CGA BCL X 102 " pdb=" O2A BCL X 102 " pdb=" CBA BCL X 102 " ideal model delta sinusoidal sigma weight residual 180.00 137.16 42.84 1 6.00e+00 2.78e-02 7.11e+01 dihedral pdb=" CBD BCL L 301 " pdb=" CGD BCL L 301 " pdb=" O2D BCL L 301 " pdb=" CED BCL L 301 " ideal model delta sinusoidal sigma weight residual 180.00 146.92 33.08 1 5.00e+00 4.00e-02 6.23e+01 ... (remaining 16073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3585 0.060 - 0.120: 487 0.120 - 0.181: 127 0.181 - 0.241: 22 0.241 - 0.301: 17 Chirality restraints: 4238 Sorted by residual: chirality pdb=" C4' LMT 3 103 " pdb=" C3' LMT 3 103 " pdb=" C5' LMT 3 103 " pdb=" O1B LMT 3 103 " both_signs ideal model delta sigma weight residual False -2.76 -2.46 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C05 PGV H 302 " pdb=" C04 PGV H 302 " pdb=" C06 PGV H 302 " pdb=" O05 PGV H 302 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C05 PGV L 311 " pdb=" C04 PGV L 311 " pdb=" C06 PGV L 311 " pdb=" O05 PGV L 311 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 4235 not shown) Planarity restraints: 4949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C33 I7D N 101 " 0.131 2.00e-02 2.50e+03 2.24e-01 5.00e+02 pdb=" C35 I7D N 101 " -0.290 2.00e-02 2.50e+03 pdb=" C36 I7D N 101 " 0.287 2.00e-02 2.50e+03 pdb=" C37 I7D N 101 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL Z 101 " 0.301 3.00e-02 1.11e+03 2.40e-01 3.21e+02 pdb=" CBA BCL Z 101 " 0.190 3.00e-02 1.11e+03 pdb=" CGA BCL Z 101 " -0.072 3.00e-02 1.11e+03 pdb=" O1A BCL Z 101 " -0.024 3.00e-02 1.11e+03 pdb=" O2A BCL Z 101 " -0.396 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL X 102 " 0.277 3.00e-02 1.11e+03 2.20e-01 2.69e+02 pdb=" CBA BCL X 102 " 0.181 3.00e-02 1.11e+03 pdb=" CGA BCL X 102 " -0.065 3.00e-02 1.11e+03 pdb=" O1A BCL X 102 " -0.035 3.00e-02 1.11e+03 pdb=" O2A BCL X 102 " -0.357 3.00e-02 1.11e+03 ... (remaining 4946 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 361 2.59 - 3.17: 23839 3.17 - 3.75: 51816 3.75 - 4.32: 76828 4.32 - 4.90: 119137 Nonbonded interactions: 271981 Sorted by model distance: nonbonded pdb=" NE2 HIS C 148 " pdb="FE HEC C 404 " model vdw 2.014 3.080 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 401 " model vdw 2.037 2.260 nonbonded pdb=" NE2 HIS L 191 " pdb="FE FE M 401 " model vdw 2.055 2.340 nonbonded pdb=" SD MET C 134 " pdb="FE HEC C 402 " model vdw 2.075 3.360 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 401 " model vdw 2.078 2.260 ... (remaining 271976 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 7 through 56) selection = (chain '2' and resid 7 through 56) selection = (chain '4' and resid 7 through 56) selection = (chain '6' and resid 7 through 56) selection = (chain '8' and resid 7 through 56) selection = (chain 'B' and resid 7 through 56) selection = (chain 'E' and resid 7 through 56) selection = (chain 'G' and resid 7 through 56) selection = (chain 'J' and resid 7 through 56) selection = (chain 'N' and resid 7 through 56) selection = (chain 'P' and resid 7 through 56) selection = (chain 'R' and resid 7 through 56) selection = (chain 'T' and resid 7 through 56) selection = (chain 'V' and resid 7 through 56) selection = (chain 'X' and resid 7 through 56) selection = (chain 'Z' and resid 7 through 56) } ncs_group { reference = (chain '1' and (resid 1 through 5 or resid 7 through 45)) selection = (chain '5' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain '7' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain '9' and (resid 1 through 5 or resid 7 through 45)) selection = (chain 'A' and (resid 1 through 5 or resid 7 through 45)) selection = (chain 'D' and (resid 1 through 5 or resid 7 through 45)) selection = (chain 'F' and (resid 1 through 5 or resid 7 through 45)) selection = (chain 'I' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'K' and (resid 1 through 5 or resid 7 through 45)) selection = (chain 'O' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'Q' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'U' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'Y' and (resid 1 through 5 or resid 7 through 45)) } ncs_group { reference = (chain '3' and resid 1 through 58) selection = (chain 'S' and (resid 1 through 45 or resid 50 through 58)) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 37 5.49 5 Mg 36 5.21 5 S 116 5.16 5 C 20373 2.51 5 N 4137 2.21 5 O 5122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 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: 0.040 Extract box with map and model: 17.240 Check model and map are aligned: 0.480 Process input model: 79.890 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Set scattering table: 0.260 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 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 : 0.023 0.216 30386 Z= 1.129 Angle : 2.955 45.998 41735 Z= 1.109 Chirality : 0.051 0.301 4238 Planarity : 0.017 0.240 4949 Dihedral : 21.403 177.598 10503 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 1.59 (0.15), residues: 2887 helix: 1.81 (0.12), residues: 1789 sheet: 0.30 (0.70), residues: 58 loop : -0.18 (0.20), residues: 1040 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 353 time to evaluate : 3.473 Fit side-chains outliers start: 31 outliers final: 19 residues processed: 371 average time/residue: 1.5055 time to fit residues: 655.5889 Evaluate side-chains 325 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 306 time to evaluate : 3.270 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 7 average time/residue: 0.4384 time to fit residues: 8.5611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.0870 chunk 218 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 137 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 69 GLN H 104 ASN H 229 GLN V 43 GLN W 45 HIS Z 20 HIS Z 43 GLN 8 43 GLN 0 43 GLN c 22 GLN g 22 GLN h 22 GLN k 22 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 30386 Z= 0.168 Angle : 1.599 25.827 41735 Z= 0.550 Chirality : 0.036 0.151 4238 Planarity : 0.004 0.064 4949 Dihedral : 23.401 178.510 5338 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.15 (0.16), residues: 2887 helix: 2.38 (0.12), residues: 1772 sheet: 0.50 (0.73), residues: 53 loop : -0.16 (0.19), residues: 1062 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 331 time to evaluate : 3.078 Fit side-chains outliers start: 54 outliers final: 24 residues processed: 356 average time/residue: 1.4008 time to fit residues: 591.7064 Evaluate side-chains 327 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 303 time to evaluate : 3.059 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 10 average time/residue: 0.7860 time to fit residues: 14.0600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 ASN H 104 ASN V 43 GLN Z 43 GLN 2 43 GLN 8 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 30386 Z= 0.242 Angle : 1.537 25.831 41735 Z= 0.538 Chirality : 0.040 0.167 4238 Planarity : 0.004 0.066 4949 Dihedral : 22.513 179.405 5338 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.16), residues: 2887 helix: 2.26 (0.12), residues: 1777 sheet: 0.44 (0.72), residues: 53 loop : -0.13 (0.20), residues: 1057 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 317 time to evaluate : 3.180 Fit side-chains outliers start: 58 outliers final: 26 residues processed: 349 average time/residue: 1.4422 time to fit residues: 598.5314 Evaluate side-chains 331 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 305 time to evaluate : 3.202 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 17 residues processed: 9 average time/residue: 0.4774 time to fit residues: 10.6424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 125 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 262 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 104 ASN Z 43 GLN 8 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 30386 Z= 0.185 Angle : 1.480 25.495 41735 Z= 0.514 Chirality : 0.037 0.159 4238 Planarity : 0.004 0.067 4949 Dihedral : 21.696 179.458 5338 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.15 (0.16), residues: 2887 helix: 2.37 (0.12), residues: 1776 sheet: 0.30 (0.70), residues: 58 loop : -0.13 (0.20), residues: 1053 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 308 time to evaluate : 3.185 Fit side-chains outliers start: 50 outliers final: 27 residues processed: 335 average time/residue: 1.4881 time to fit residues: 594.3857 Evaluate side-chains 330 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 303 time to evaluate : 3.095 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 18 residues processed: 9 average time/residue: 0.9528 time to fit residues: 15.5814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 104 ASN E 43 GLN Z 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 30386 Z= 0.301 Angle : 1.535 25.732 41735 Z= 0.541 Chirality : 0.042 0.203 4238 Planarity : 0.005 0.068 4949 Dihedral : 22.185 178.377 5338 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 1.96 (0.15), residues: 2887 helix: 2.18 (0.12), residues: 1764 sheet: 0.12 (0.70), residues: 58 loop : -0.10 (0.20), residues: 1065 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 308 time to evaluate : 3.363 Fit side-chains outliers start: 56 outliers final: 25 residues processed: 343 average time/residue: 1.4511 time to fit residues: 588.6110 Evaluate side-chains 326 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 301 time to evaluate : 3.397 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 19 residues processed: 6 average time/residue: 0.5689 time to fit residues: 9.1293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 7.9990 chunk 250 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 278 optimal weight: 7.9990 chunk 231 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 104 ASN H 246 HIS E 43 GLN Z 43 GLN 4 20 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 30386 Z= 0.160 Angle : 1.463 25.185 41735 Z= 0.506 Chirality : 0.037 0.166 4238 Planarity : 0.004 0.068 4949 Dihedral : 21.097 178.720 5338 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.19 (0.16), residues: 2887 helix: 2.41 (0.12), residues: 1777 sheet: 0.21 (0.70), residues: 58 loop : -0.14 (0.20), residues: 1052 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 309 time to evaluate : 3.693 Fit side-chains outliers start: 47 outliers final: 22 residues processed: 340 average time/residue: 1.4126 time to fit residues: 573.4907 Evaluate side-chains 316 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 294 time to evaluate : 3.121 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 17 residues processed: 6 average time/residue: 0.5118 time to fit residues: 8.3774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 203 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 277 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 ASN H 104 ASN E 43 GLN 4 20 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 30386 Z= 0.209 Angle : 1.482 24.792 41735 Z= 0.517 Chirality : 0.038 0.160 4238 Planarity : 0.004 0.067 4949 Dihedral : 21.137 178.163 5338 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.15 (0.16), residues: 2887 helix: 2.36 (0.12), residues: 1770 sheet: 0.25 (0.70), residues: 58 loop : -0.09 (0.20), residues: 1059 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 300 time to evaluate : 3.365 Fit side-chains outliers start: 41 outliers final: 23 residues processed: 328 average time/residue: 1.4387 time to fit residues: 560.2010 Evaluate side-chains 315 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 292 time to evaluate : 2.970 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 6 average time/residue: 0.6002 time to fit residues: 8.9907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 176 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 ASN H 104 ASN E 43 GLN 4 20 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 30386 Z= 0.154 Angle : 1.443 24.103 41735 Z= 0.499 Chirality : 0.036 0.168 4238 Planarity : 0.004 0.067 4949 Dihedral : 20.330 179.868 5338 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.30 (0.16), residues: 2887 helix: 2.51 (0.12), residues: 1773 sheet: 0.28 (0.70), residues: 58 loop : -0.12 (0.20), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 305 time to evaluate : 3.239 Fit side-chains outliers start: 33 outliers final: 21 residues processed: 328 average time/residue: 1.4634 time to fit residues: 573.0621 Evaluate side-chains 314 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 293 time to evaluate : 3.082 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 16 residues processed: 6 average time/residue: 0.3662 time to fit residues: 7.4376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 257 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 ASN H 104 ASN E 43 GLN 2 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 30386 Z= 0.237 Angle : 1.488 25.049 41735 Z= 0.521 Chirality : 0.040 0.169 4238 Planarity : 0.004 0.066 4949 Dihedral : 20.911 179.569 5338 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.12 (0.16), residues: 2887 helix: 2.33 (0.12), residues: 1770 sheet: 0.29 (0.70), residues: 58 loop : -0.10 (0.20), residues: 1059 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 295 time to evaluate : 3.210 Fit side-chains outliers start: 36 outliers final: 25 residues processed: 318 average time/residue: 1.4397 time to fit residues: 545.5115 Evaluate side-chains 314 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 289 time to evaluate : 3.386 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 19 residues processed: 8 average time/residue: 0.5465 time to fit residues: 10.3072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.7980 chunk 273 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 190 optimal weight: 0.3980 chunk 286 optimal weight: 5.9990 chunk 264 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 176 optimal weight: 0.0000 chunk 140 optimal weight: 0.0670 overall best weight: 0.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN C 200 ASN H 104 ASN E 43 GLN 6 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 30386 Z= 0.144 Angle : 1.437 23.956 41735 Z= 0.497 Chirality : 0.036 0.171 4238 Planarity : 0.004 0.065 4949 Dihedral : 20.093 177.594 5338 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.31 (0.16), residues: 2887 helix: 2.54 (0.12), residues: 1771 sheet: 0.49 (0.73), residues: 53 loop : -0.15 (0.20), residues: 1063 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 303 time to evaluate : 3.245 Fit side-chains outliers start: 25 outliers final: 20 residues processed: 322 average time/residue: 1.4392 time to fit residues: 554.6096 Evaluate side-chains 313 residues out of total 2452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 293 time to evaluate : 3.008 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 4 average time/residue: 0.4473 time to fit residues: 6.6973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 210 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 chunk 228 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN C 200 ASN H 104 ASN E 43 GLN 6 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.090806 restraints weight = 53198.553| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.84 r_work: 0.2815 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 30386 Z= 0.176 Angle : 1.454 24.446 41735 Z= 0.504 Chirality : 0.037 0.167 4238 Planarity : 0.004 0.065 4949 Dihedral : 20.177 176.644 5338 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.16), residues: 2887 helix: 2.48 (0.12), residues: 1771 sheet: 0.48 (0.72), residues: 53 loop : -0.13 (0.20), residues: 1063 =============================================================================== Job complete usr+sys time: 10379.88 seconds wall clock time: 186 minutes 1.24 seconds (11161.24 seconds total)