Starting phenix.real_space_refine (version: dev) on Thu Dec 22 01:29:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/12_2022/7pqd_13590_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/12_2022/7pqd_13590.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/12_2022/7pqd_13590_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/12_2022/7pqd_13590_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/12_2022/7pqd_13590_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/12_2022/7pqd_13590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/12_2022/7pqd_13590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/12_2022/7pqd_13590_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/12_2022/7pqd_13590_updated.pdb" } resolution = 2.9 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= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "BD PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bd PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 45952 Number of models: 1 Model: "" Number of chains: 144 Chain: "AA" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 394 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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: "AB" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "AC" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "AD" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "AE" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "AF" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "AG" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "AH" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "AI" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "AJ" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "AK" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "AL" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "AM" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "AN" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 432 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "BA" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BB" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BC" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "BD" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BE" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BF" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BG" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BH" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BI" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BJ" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BK" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "BL" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "BM" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "BN" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "H" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1866 Classifications: {'peptide': 246} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 222} Chain: "L" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2231 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2444 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "UA" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "UB" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "UU" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 362 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "X" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "aa" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 394 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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: "ab" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "ac" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "ad" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "ae" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "af" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "ag" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "ah" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "ai" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "aj" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "ak" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "al" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "am" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, '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: "an" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 432 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "ba" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bb" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bc" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "bd" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "be" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bf" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bg" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bh" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bi" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bj" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bk" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "bl" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "bm" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "bn" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "h" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1866 Classifications: {'peptide': 246} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 222} Chain: "l" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2231 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "m" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2444 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "ua" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "ub" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "uu" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 362 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "x" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "AA" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AB" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SP2': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AC" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 201 Unusual residues: {'3PE': 1, 'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AD" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "AE" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AF" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AG" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AH" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AI" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AJ" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AK" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AL" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "AM" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AN" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BB" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BC" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BD" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BE" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BF" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BG" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BH" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BI" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BJ" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BK" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BL" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BM" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BN" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 135 Unusual residues: {'3PE': 1, 'CD4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 332 Unusual residues: {'BCL': 2, 'BPH': 1, 'SQD': 1, 'U10': 1, 'UQ1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 422 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CD4': 1, 'LMT': 1, 'SP2': 1, 'U10': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "aa" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ab" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SP2': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "ac" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 201 Unusual residues: {'3PE': 1, 'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "ad" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ae" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "af" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SP2': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "ag" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ah" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ai" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "aj" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "ak" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "al" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "am" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "an" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ba" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bb" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bc" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "bd" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "be" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "bf" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bg" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "bh" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bi" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "bj" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bk" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bl" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bm" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "bn" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 135 Unusual residues: {'3PE': 1, 'CD4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 278 Unusual residues: {'BCL': 2, 'BPH': 1, 'U10': 1, 'UQ1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "m" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 422 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CD4': 1, 'LMT': 1, 'SP2': 1, 'U10': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "x" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'SQD': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "BB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "M" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "X" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "ab" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "l" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "m" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "x" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 24.50, per 1000 atoms: 0.53 Number of scatterers: 45952 At special positions: 0 Unit cell: (144.95, 225.55, 106.6, 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 2 26.01 S 202 16.00 P 12 15.00 Mg 64 11.99 O 6956 8.00 N 6388 7.00 C 32328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=64, symmetry=0 Number of additional bonds: simple=64, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.15 Conformation dependent library (CDL) restraints added in 5.2 seconds 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 8 sheets defined 66.4% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'AA' and resid 4 through 10 Processing helix chain 'AA' and resid 13 through 36 Processing helix chain 'AA' and resid 39 through 41 No H-bonds generated for 'chain 'AA' and resid 39 through 41' Processing helix chain 'AB' and resid 4 through 10 Processing helix chain 'AB' and resid 13 through 36 removed outlier: 3.659A pdb=" N VALAB 18 " --> pdb=" O ARGAB 14 " (cutoff:3.500A) Processing helix chain 'AB' and resid 43 through 50 Processing helix chain 'AC' and resid 3 through 10 Processing helix chain 'AC' and resid 13 through 36 Processing helix chain 'AC' and resid 43 through 50 Processing helix chain 'AD' and resid 4 through 10 Processing helix chain 'AD' and resid 13 through 36 Processing helix chain 'AD' and resid 43 through 50 Processing helix chain 'AE' and resid 3 through 10 Processing helix chain 'AE' and resid 13 through 37 Processing helix chain 'AE' and resid 43 through 50 removed outlier: 3.529A pdb=" N ALAAE 48 " --> pdb=" O LEUAE 44 " (cutoff:3.500A) Processing helix chain 'AF' and resid 4 through 10 Processing helix chain 'AF' and resid 13 through 37 Processing helix chain 'AF' and resid 43 through 50 Processing helix chain 'AG' and resid 4 through 10 Processing helix chain 'AG' and resid 13 through 37 removed outlier: 3.786A pdb=" N VALAG 18 " --> pdb=" O ARGAG 14 " (cutoff:3.500A) Processing helix chain 'AG' and resid 43 through 50 Processing helix chain 'AH' and resid 4 through 9 Processing helix chain 'AH' and resid 13 through 36 Processing helix chain 'AH' and resid 43 through 50 Processing helix chain 'AI' and resid 4 through 10 Processing helix chain 'AI' and resid 13 through 36 Processing helix chain 'AI' and resid 43 through 50 Processing helix chain 'AJ' and resid 4 through 9 Processing helix chain 'AJ' and resid 13 through 37 Processing helix chain 'AJ' and resid 43 through 50 Processing helix chain 'AK' and resid 3 through 9 Processing helix chain 'AK' and resid 13 through 37 Processing helix chain 'AK' and resid 43 through 50 Processing helix chain 'AL' and resid 4 through 9 Processing helix chain 'AL' and resid 13 through 36 Processing helix chain 'AL' and resid 43 through 50 Processing helix chain 'AM' and resid 3 through 10 Processing helix chain 'AM' and resid 13 through 37 removed outlier: 3.724A pdb=" N ALAAM 19 " --> pdb=" O ARGAM 15 " (cutoff:3.500A) Processing helix chain 'AM' and resid 43 through 50 Processing helix chain 'AN' and resid 5 through 10 Processing helix chain 'AN' and resid 13 through 37 removed outlier: 3.519A pdb=" N VALAN 22 " --> pdb=" O VALAN 18 " (cutoff:3.500A) Processing helix chain 'AN' and resid 43 through 50 removed outlier: 3.810A pdb=" N ALAAN 49 " --> pdb=" O GLUAN 45 " (cutoff:3.500A) Processing helix chain 'BA' and resid 14 through 45 removed outlier: 3.508A pdb=" N SERBA 22 " --> pdb=" O GLNBA 18 " (cutoff:3.500A) Processing helix chain 'BB' and resid 14 through 45 Processing helix chain 'BC' and resid 14 through 45 Processing helix chain 'BD' and resid 14 through 45 Processing helix chain 'BE' and resid 14 through 45 Processing helix chain 'BF' and resid 14 through 45 Processing helix chain 'BG' and resid 14 through 45 Processing helix chain 'BH' and resid 14 through 45 Processing helix chain 'BI' and resid 14 through 45 Processing helix chain 'BJ' and resid 14 through 45 removed outlier: 3.640A pdb=" N SERBJ 22 " --> pdb=" O GLNBJ 18 " (cutoff:3.500A) Processing helix chain 'BK' and resid 14 through 45 Processing helix chain 'BL' and resid 14 through 46 removed outlier: 3.693A pdb=" N SERBL 22 " --> pdb=" O GLNBL 18 " (cutoff:3.500A) Processing helix chain 'BM' and resid 14 through 46 removed outlier: 3.615A pdb=" N TRPBM 45 " --> pdb=" O ALABM 41 " (cutoff:3.500A) Processing helix chain 'BN' and resid 14 through 45 removed outlier: 3.645A pdb=" N VALBN 34 " --> pdb=" O LEUBN 30 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEUBN 40 " --> pdb=" O ILEBN 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 36 Processing helix chain 'H' and resid 104 through 107 No H-bonds generated for 'chain 'H' and resid 104 through 107' Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 210 through 215 removed outlier: 3.783A pdb=" N PHE H 213 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 243 removed outlier: 4.090A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 32 through 56 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 84 through 111 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.669A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 152 through 164 removed outlier: 4.115A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 225 through 249 removed outlier: 3.891A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 267 Processing helix chain 'M' and resid 26 through 28 No H-bonds generated for 'chain 'M' and resid 26 through 28' Processing helix chain 'M' and resid 37 through 41 removed outlier: 3.562A pdb=" N TRP M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 37 through 41' Processing helix chain 'M' and resid 53 through 77 Processing helix chain 'M' and resid 82 through 87 removed outlier: 3.576A pdb=" N LEU M 86 " --> pdb=" O PRO M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 101 No H-bonds generated for 'chain 'M' and resid 99 through 101' 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 140 removed outlier: 3.728A pdb=" N ALA M 137 " --> pdb=" O THR M 133 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 161 removed outlier: 3.666A pdb=" N SER M 152 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU M 156 " --> pdb=" O SER M 152 " (cutoff:3.500A) 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 removed outlier: 3.772A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) 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 225 Processing helix chain 'M' and resid 227 through 229 No H-bonds generated for 'chain 'M' and resid 227 through 229' Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 256 removed outlier: 3.532A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 285 removed outlier: 3.887A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.250A 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 'UA' and resid 2 through 28 Processing helix chain 'UB' and resid 4 through 27 Processing helix chain 'UU' and resid 6 through 29 removed outlier: 3.832A pdb=" N VALUU 16 " --> pdb=" O METUU 12 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VALUU 19 " --> pdb=" O ALAUU 15 " (cutoff:3.500A) Processing helix chain 'UU' and resid 32 through 47 Processing helix chain 'X' and resid 16 through 54 Processing helix chain 'aa' and resid 4 through 10 Processing helix chain 'aa' and resid 13 through 36 Processing helix chain 'aa' and resid 39 through 41 No H-bonds generated for 'chain 'aa' and resid 39 through 41' Processing helix chain 'ab' and resid 4 through 10 Processing helix chain 'ab' and resid 13 through 36 removed outlier: 3.532A pdb=" N VALab 18 " --> pdb=" O ARGab 14 " (cutoff:3.500A) Processing helix chain 'ab' and resid 43 through 50 Processing helix chain 'ac' and resid 3 through 10 Processing helix chain 'ac' and resid 13 through 36 Processing helix chain 'ac' and resid 43 through 50 Processing helix chain 'ad' and resid 4 through 10 Processing helix chain 'ad' and resid 13 through 36 Processing helix chain 'ad' and resid 43 through 50 Processing helix chain 'ae' and resid 3 through 10 Processing helix chain 'ae' and resid 13 through 37 Processing helix chain 'ae' and resid 43 through 50 removed outlier: 3.530A pdb=" N ALAae 48 " --> pdb=" O LEUae 44 " (cutoff:3.500A) Processing helix chain 'af' and resid 4 through 10 Processing helix chain 'af' and resid 13 through 37 Processing helix chain 'af' and resid 43 through 50 Processing helix chain 'ag' and resid 4 through 10 Processing helix chain 'ag' and resid 13 through 37 removed outlier: 3.799A pdb=" N VALag 18 " --> pdb=" O ARGag 14 " (cutoff:3.500A) Processing helix chain 'ag' and resid 43 through 50 Processing helix chain 'ah' and resid 4 through 9 removed outlier: 3.547A pdb=" N ILEah 7 " --> pdb=" O PHEah 4 " (cutoff:3.500A) Processing helix chain 'ah' and resid 13 through 36 Processing helix chain 'ah' and resid 43 through 50 Processing helix chain 'ai' and resid 4 through 10 Processing helix chain 'ai' and resid 13 through 36 Processing helix chain 'ai' and resid 43 through 50 Processing helix chain 'aj' and resid 4 through 9 Processing helix chain 'aj' and resid 13 through 37 Processing helix chain 'aj' and resid 43 through 50 Processing helix chain 'ak' and resid 3 through 9 Processing helix chain 'ak' and resid 13 through 37 Processing helix chain 'ak' and resid 43 through 50 Processing helix chain 'al' and resid 4 through 9 Processing helix chain 'al' and resid 13 through 36 Processing helix chain 'al' and resid 43 through 50 Processing helix chain 'am' and resid 3 through 10 Processing helix chain 'am' and resid 13 through 37 removed outlier: 3.723A pdb=" N ALAam 19 " --> pdb=" O ARGam 15 " (cutoff:3.500A) Processing helix chain 'am' and resid 43 through 50 Processing helix chain 'an' and resid 5 through 10 Processing helix chain 'an' and resid 13 through 37 removed outlier: 3.519A pdb=" N VALan 22 " --> pdb=" O VALan 18 " (cutoff:3.500A) Processing helix chain 'an' and resid 43 through 50 removed outlier: 3.812A pdb=" N ALAan 49 " --> pdb=" O GLUan 45 " (cutoff:3.500A) Processing helix chain 'ba' and resid 14 through 45 removed outlier: 3.547A pdb=" N SERba 22 " --> pdb=" O GLNba 18 " (cutoff:3.500A) Processing helix chain 'bb' and resid 14 through 45 Processing helix chain 'bc' and resid 14 through 45 Processing helix chain 'bd' and resid 14 through 45 Processing helix chain 'be' and resid 14 through 45 Processing helix chain 'bf' and resid 14 through 45 Processing helix chain 'bg' and resid 14 through 45 Processing helix chain 'bh' and resid 14 through 45 Processing helix chain 'bi' and resid 14 through 45 Processing helix chain 'bj' and resid 14 through 45 removed outlier: 3.640A pdb=" N SERbj 22 " --> pdb=" O GLNbj 18 " (cutoff:3.500A) Processing helix chain 'bk' and resid 14 through 45 Processing helix chain 'bl' and resid 14 through 46 removed outlier: 3.692A pdb=" N SERbl 22 " --> pdb=" O GLNbl 18 " (cutoff:3.500A) Processing helix chain 'bm' and resid 14 through 46 removed outlier: 3.617A pdb=" N TRPbm 45 " --> pdb=" O ALAbm 41 " (cutoff:3.500A) Processing helix chain 'bn' and resid 14 through 45 removed outlier: 3.647A pdb=" N VALbn 34 " --> pdb=" O LEUbn 30 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEUbn 40 " --> pdb=" O ILEbn 36 " (cutoff:3.500A) Processing helix chain 'h' and resid 12 through 36 Processing helix chain 'h' and resid 104 through 107 No H-bonds generated for 'chain 'h' and resid 104 through 107' Processing helix chain 'h' and resid 110 through 112 No H-bonds generated for 'chain 'h' and resid 110 through 112' Processing helix chain 'h' and resid 134 through 136 No H-bonds generated for 'chain 'h' and resid 134 through 136' Processing helix chain 'h' and resid 193 through 195 No H-bonds generated for 'chain 'h' and resid 193 through 195' Processing helix chain 'h' and resid 210 through 215 removed outlier: 3.781A pdb=" N PHE h 213 " --> pdb=" O SER h 210 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA h 214 " --> pdb=" O ASP h 211 " (cutoff:3.500A) Processing helix chain 'h' and resid 227 through 243 removed outlier: 4.092A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'l' and resid 7 through 9 No H-bonds generated for 'chain 'l' and resid 7 through 9' Processing helix chain 'l' and resid 32 through 56 Processing helix chain 'l' and resid 71 through 73 No H-bonds generated for 'chain 'l' and resid 71 through 73' Processing helix chain 'l' and resid 80 through 82 No H-bonds generated for 'chain 'l' and resid 80 through 82' Processing helix chain 'l' and resid 84 through 111 Processing helix chain 'l' and resid 116 through 132 removed outlier: 3.669A pdb=" N PHE l 123 " --> pdb=" O PHE l 119 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Processing helix chain 'l' and resid 134 through 139 Processing helix chain 'l' and resid 142 through 144 No H-bonds generated for 'chain 'l' and resid 142 through 144' Processing helix chain 'l' and resid 152 through 164 removed outlier: 4.114A pdb=" N TYR l 164 " --> pdb=" O THR l 160 " (cutoff:3.500A) Processing helix chain 'l' and resid 167 through 169 No H-bonds generated for 'chain 'l' and resid 167 through 169' Processing helix chain 'l' and resid 171 through 198 Processing helix chain 'l' and resid 209 through 220 Processing helix chain 'l' and resid 225 through 249 removed outlier: 3.891A pdb=" N HIS l 230 " --> pdb=" O THR l 226 " (cutoff:3.500A) Processing helix chain 'l' and resid 259 through 267 Processing helix chain 'm' and resid 26 through 28 No H-bonds generated for 'chain 'm' and resid 26 through 28' Processing helix chain 'm' and resid 37 through 41 removed outlier: 3.561A pdb=" N TRP m 41 " --> pdb=" O THR m 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 37 through 41' Processing helix chain 'm' and resid 53 through 77 Processing helix chain 'm' and resid 82 through 87 removed outlier: 3.577A pdb=" N LEU m 86 " --> pdb=" O PRO m 82 " (cutoff:3.500A) Processing helix chain 'm' and resid 99 through 101 No H-bonds generated for 'chain 'm' and resid 99 through 101' 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 140 removed outlier: 3.731A pdb=" N ALA m 137 " --> pdb=" O THR m 133 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU m 140 " --> pdb=" O ARG m 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 145 through 161 removed outlier: 3.665A pdb=" N SER m 152 " --> pdb=" O TRP m 148 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA m 153 " --> pdb=" O ALA m 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU m 156 " --> pdb=" O SER m 152 " (cutoff:3.500A) 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 removed outlier: 3.778A pdb=" N LEU m 183 " --> pdb=" O ILE m 179 " (cutoff:3.500A) 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 225 Processing helix chain 'm' and resid 227 through 229 No H-bonds generated for 'chain 'm' and resid 227 through 229' Processing helix chain 'm' and resid 234 through 239 Processing helix chain 'm' and resid 243 through 256 removed outlier: 3.531A pdb=" N TRP m 252 " --> pdb=" O ALA m 248 " (cutoff:3.500A) Processing helix chain 'm' and resid 265 through 285 removed outlier: 3.889A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 4.249A 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 'ua' and resid 2 through 28 Processing helix chain 'ub' and resid 4 through 27 Processing helix chain 'uu' and resid 6 through 29 removed outlier: 3.831A pdb=" N VALuu 16 " --> pdb=" O METuu 12 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VALuu 19 " --> pdb=" O ALAuu 15 " (cutoff:3.500A) Processing helix chain 'uu' and resid 32 through 47 Processing helix chain 'x' and resid 16 through 54 Processing sheet with id= A, first strand: chain 'H' and resid 62 through 65 Processing sheet with id= B, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.827A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 203 through 205 removed outlier: 3.616A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY H 155 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE H 160 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'h' and resid 62 through 65 Processing sheet with id= F, first strand: chain 'h' and resid 87 through 89 Processing sheet with id= G, first strand: chain 'h' and resid 131 through 133 removed outlier: 6.827A pdb=" N GLU h 180 " --> pdb=" O VAL h 165 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE h 167 " --> pdb=" O PHE h 178 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE h 178 " --> pdb=" O ILE h 167 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'h' and resid 203 through 205 removed outlier: 3.617A pdb=" N GLY h 162 " --> pdb=" O VAL h 153 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY h 155 " --> pdb=" O ILE h 160 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE h 160 " --> pdb=" O GLY h 155 " (cutoff:3.500A) 2351 hydrogen bonds defined for protein. 6672 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: 14.74 Time building geometry restraints manager: 20.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 13109 1.37 - 1.57: 33775 1.57 - 1.78: 88 1.78 - 1.99: 334 1.99 - 2.19: 256 Bond restraints: 47562 Sorted by residual: bond pdb=" C6 SQD L 306 " pdb=" S SQD L 306 " ideal model delta sigma weight residual 1.840 1.614 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C6 SQD x 100 " pdb=" S SQD x 100 " ideal model delta sigma weight residual 1.840 1.615 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" O7 SQD x 100 " pdb=" S SQD x 100 " ideal model delta sigma weight residual 1.509 1.298 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" O7 SQD L 306 " pdb=" S SQD L 306 " ideal model delta sigma weight residual 1.509 1.298 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" O9 SQD x 100 " pdb=" S SQD x 100 " ideal model delta sigma weight residual 1.511 1.304 0.207 2.00e-02 2.50e+03 1.07e+02 ... (remaining 47557 not shown) Histogram of bond angle deviations from ideal: 84.27 - 99.25: 260 99.25 - 114.23: 27768 114.23 - 129.21: 35851 129.21 - 144.18: 1133 144.18 - 159.16: 196 Bond angle restraints: 65208 Sorted by residual: angle pdb=" C19 SP2AE 101 " pdb=" C18 SP2AE 101 " pdb=" CM6 SP2AE 101 " ideal model delta sigma weight residual 68.22 118.19 -49.97 3.00e+00 1.11e-01 2.77e+02 angle pdb=" C19 SP2ae 102 " pdb=" C18 SP2ae 102 " pdb=" CM6 SP2ae 102 " ideal model delta sigma weight residual 68.22 118.13 -49.91 3.00e+00 1.11e-01 2.77e+02 angle pdb=" C19 SP2AJ 102 " pdb=" C18 SP2AJ 102 " pdb=" CM6 SP2AJ 102 " ideal model delta sigma weight residual 68.22 118.11 -49.89 3.00e+00 1.11e-01 2.77e+02 angle pdb=" C19 SP2AB 102 " pdb=" C18 SP2AB 102 " pdb=" CM6 SP2AB 102 " ideal model delta sigma weight residual 68.22 118.09 -49.87 3.00e+00 1.11e-01 2.76e+02 angle pdb=" C19 SP2am1000 " pdb=" C18 SP2am1000 " pdb=" CM6 SP2am1000 " ideal model delta sigma weight residual 68.22 118.08 -49.86 3.00e+00 1.11e-01 2.76e+02 ... (remaining 65203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 24116 35.94 - 71.88: 805 71.88 - 107.82: 145 107.82 - 143.76: 24 143.76 - 179.70: 18 Dihedral angle restraints: 25108 sinusoidal: 11534 harmonic: 13574 Sorted by residual: dihedral pdb=" C1 BCLac 102 " pdb=" C2 BCLac 102 " pdb=" C3 BCLac 102 " pdb=" C5 BCLac 102 " ideal model delta sinusoidal sigma weight residual 180.00 0.30 179.70 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCLAC 101 " pdb=" C2 BCLAC 101 " pdb=" C3 BCLAC 101 " pdb=" C5 BCLAC 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.98 179.02 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCLAN 101 " pdb=" C2 BCLAN 101 " pdb=" C3 BCLAN 101 " pdb=" C5 BCLAN 101 " ideal model delta sinusoidal sigma weight residual -180.00 -1.20 -178.80 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 25105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.981: 6384 0.981 - 1.962: 0 1.962 - 2.943: 0 2.943 - 3.924: 0 3.924 - 4.904: 2 Chirality restraints: 6386 Sorted by residual: chirality pdb=" C1 SQD L 306 " pdb=" C2 SQD L 306 " pdb=" O5 SQD L 306 " pdb=" O6 SQD L 306 " both_signs ideal model delta sigma weight residual False -2.39 2.52 -4.90 2.00e-01 2.50e+01 6.01e+02 chirality pdb=" C1 SQD x 100 " pdb=" C2 SQD x 100 " pdb=" O5 SQD x 100 " pdb=" O6 SQD x 100 " both_signs ideal model delta sigma weight residual False -2.39 2.46 -4.85 2.00e-01 2.50e+01 5.89e+02 chirality pdb=" C2C BPH M1003 " pdb=" C1C BPH M1003 " pdb=" C3C BPH M1003 " pdb=" CMC BPH M1003 " both_signs ideal model delta sigma weight residual False -2.81 -2.59 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 6383 not shown) Planarity restraints: 7950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C24 SP2AK 102 " -0.095 2.00e-02 2.50e+03 8.03e-02 8.06e+01 pdb=" C25 SP2AK 102 " 0.125 2.00e-02 2.50e+03 pdb=" C26 SP2AK 102 " 0.042 2.00e-02 2.50e+03 pdb=" C27 SP2AK 102 " -0.077 2.00e-02 2.50e+03 pdb=" CM8 SP2AK 102 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C24 SP2ak 102 " 0.094 2.00e-02 2.50e+03 7.94e-02 7.88e+01 pdb=" C25 SP2ak 102 " -0.123 2.00e-02 2.50e+03 pdb=" C26 SP2ak 102 " -0.041 2.00e-02 2.50e+03 pdb=" C27 SP2ak 102 " 0.076 2.00e-02 2.50e+03 pdb=" CM8 SP2ak 102 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 SP2AA1002 " 0.062 2.00e-02 2.50e+03 6.45e-02 5.20e+01 pdb=" C5 SP2AA1002 " -0.035 2.00e-02 2.50e+03 pdb=" C6 SP2AA1002 " -0.096 2.00e-02 2.50e+03 pdb=" C7 SP2AA1002 " 0.080 2.00e-02 2.50e+03 pdb=" CM3 SP2AA1002 " -0.010 2.00e-02 2.50e+03 ... (remaining 7947 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 284 2.63 - 3.20: 38773 3.20 - 3.77: 74226 3.77 - 4.33: 110370 4.33 - 4.90: 172538 Nonbonded interactions: 396191 Sorted by model distance: nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M1006 " model vdw 2.065 2.260 nonbonded pdb=" OE2 GLU m 234 " pdb="FE FE m1008 " model vdw 2.065 2.260 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M1006 " model vdw 2.106 2.260 nonbonded pdb=" OE1 GLU m 234 " pdb="FE FE m1008 " model vdw 2.106 2.260 nonbonded pdb=" NE2 HIS l 190 " pdb="FE FE m1008 " model vdw 2.254 2.340 ... (remaining 396186 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 'AA' and resid 4 through 46) selection = (chain 'AD' and resid 4 through 46) selection = (chain 'AL' and resid 4 through 46) selection = (chain 'AN' and resid 4 through 46) selection = (chain 'aa' and resid 4 through 46) selection = (chain 'ag' and resid 4 through 46) selection = (chain 'an' and resid 4 through 46) } ncs_group { reference = (chain 'AB' and resid 1 through 55) selection = (chain 'AC' and resid 1 through 55) selection = (chain 'AE' and resid 1 through 55) selection = (chain 'AF' and resid 1 through 55) selection = (chain 'AG' and resid 1 through 55) selection = (chain 'AH' and resid 1 through 55) selection = (chain 'AI' and resid 1 through 55) selection = (chain 'AJ' and resid 1 through 55) selection = (chain 'AK' and resid 1 through 55) selection = (chain 'AM' and resid 1 through 55) selection = (chain 'ab' and resid 1 through 55) selection = (chain 'ac' and resid 1 through 55) selection = (chain 'ad' and resid 1 through 55) selection = (chain 'ae' and resid 1 through 55) selection = (chain 'af' and resid 1 through 55) selection = (chain 'ah' and resid 1 through 55) selection = (chain 'ai' and resid 1 through 55) selection = (chain 'aj' and resid 1 through 55) selection = (chain 'ak' and resid 1 through 55) selection = (chain 'al' and resid 1 through 55) selection = (chain 'am' and resid 1 through 55) } ncs_group { reference = (chain 'BA' and resid 8 through 49) selection = (chain 'BB' and resid 8 through 49) selection = (chain 'BC' and resid 8 through 49) selection = (chain 'BD' and resid 8 through 49) selection = (chain 'BE' and resid 8 through 49) selection = (chain 'BF' and resid 8 through 49) selection = (chain 'BG' and resid 8 through 49) selection = (chain 'BH' and resid 8 through 49) selection = (chain 'BI' and resid 8 through 49) selection = (chain 'BJ' and resid 8 through 49) selection = (chain 'BK' and resid 8 through 49) selection = (chain 'BL' and resid 8 through 49) selection = (chain 'BM' and resid 8 through 49) selection = (chain 'ba' and resid 8 through 49) selection = (chain 'bb' and resid 8 through 49) selection = (chain 'bc' and resid 8 through 49) selection = (chain 'bd' and resid 8 through 49) selection = (chain 'be' and resid 8 through 49) selection = (chain 'bf' and resid 8 through 49) selection = (chain 'bg' and resid 8 through 49) selection = (chain 'bh' and resid 8 through 49) selection = (chain 'bi' and resid 8 through 49) selection = (chain 'bj' and resid 8 through 49) selection = (chain 'bk' and resid 8 through 49) selection = (chain 'bl' and resid 8 through 49) selection = (chain 'bm' and resid 8 through 49) } ncs_group { reference = chain 'BN' selection = chain 'bn' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = (chain 'L' and (resid 1 through 281 or resid 301 or resid 303)) selection = (chain 'l' and (resid 1 through 281 or resid 301 or resid 303)) } ncs_group { reference = (chain 'M' and (resid 1 through 307 or resid 1001)) selection = (chain 'm' and (resid 1 through 307 or resid 1001)) } ncs_group { reference = chain 'UA' selection = chain 'UB' selection = chain 'ua' selection = chain 'ub' } ncs_group { reference = chain 'UU' selection = chain 'uu' } ncs_group { reference = chain 'X' selection = (chain 'x' and resid 15 through 69) } 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 2 7.16 5 P 12 5.49 5 Mg 64 5.21 5 S 202 5.16 5 C 32328 2.51 5 N 6388 2.21 5 O 6956 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.550 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: 30.140 Check model and map are aligned: 0.720 Convert atoms to be neutral: 0.350 Process input model: 107.910 Find NCS groups from input model: 3.760 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.016 0.226 47562 Z= 0.822 Angle : 4.872 49.974 65208 Z= 1.650 Chirality : 0.097 4.904 6386 Planarity : 0.009 0.121 7950 Dihedral : 18.968 179.702 16384 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.18 % Favored : 97.73 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.11), residues: 4532 helix: -0.34 (0.08), residues: 3198 sheet: 0.11 (0.66), residues: 44 loop : -0.05 (0.17), residues: 1290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 843 time to evaluate : 4.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 853 average time/residue: 1.3292 time to fit residues: 1450.2235 Evaluate side-chains 679 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 677 time to evaluate : 4.460 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 5.5634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 1.9990 chunk 335 optimal weight: 5.9990 chunk 185 optimal weight: 0.2980 chunk 114 optimal weight: 5.9990 chunk 225 optimal weight: 0.7980 chunk 178 optimal weight: 6.9990 chunk 346 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 401 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 20 GLN AB 20 GLN AE 20 GLN AF 52 ASN ** AJ 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 42 ASN BK 21 HIS H 52 ASN H 147 ASN L 183 ASN M 188 ASN M 293 ASN X 58 GLN aa 20 GLN ab 20 GLN ae 20 GLN af 52 ASN aj 20 GLN ** aj 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ak 42 ASN bd 16 GLN h 52 ASN h 147 ASN l 183 ASN m 188 ASN m 293 ASN x 58 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 47562 Z= 0.203 Angle : 2.582 32.281 65208 Z= 0.877 Chirality : 0.039 0.216 6386 Planarity : 0.004 0.036 7950 Dihedral : 20.355 179.900 8276 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 (0.12), residues: 4532 helix: 1.89 (0.09), residues: 3130 sheet: 0.79 (0.71), residues: 44 loop : 0.50 (0.18), residues: 1358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 710 time to evaluate : 4.532 Fit side-chains revert: symmetry clash outliers start: 99 outliers final: 28 residues processed: 747 average time/residue: 1.3161 time to fit residues: 1266.1978 Evaluate side-chains 688 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 660 time to evaluate : 4.451 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 16 residues processed: 16 average time/residue: 1.0335 time to fit residues: 27.8671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 334 optimal weight: 8.9990 chunk 273 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 402 optimal weight: 7.9990 chunk 434 optimal weight: 4.9990 chunk 358 optimal weight: 6.9990 chunk 398 optimal weight: 8.9990 chunk 137 optimal weight: 0.0980 chunk 322 optimal weight: 9.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 20 GLN AD 20 GLN AE 20 GLN AI 20 GLN AJ 20 GLN ** AJ 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN BF 18 GLN BG 21 HIS BK 21 HIS H 32 GLN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN M 188 ASN M 300 ASN X 58 GLN ac 20 GLN ad 20 GLN ae 20 GLN ** ai 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** aj 20 GLN ** aj 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** al 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bd 16 GLN bg 21 HIS h 32 GLN ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 60 ASN m 188 ASN m 300 ASN x 58 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.094 47562 Z= 0.473 Angle : 2.581 30.962 65208 Z= 0.887 Chirality : 0.049 0.278 6386 Planarity : 0.006 0.042 7950 Dihedral : 20.766 180.000 8276 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.26 (0.12), residues: 4532 helix: 1.29 (0.09), residues: 3132 sheet: 0.66 (0.68), residues: 44 loop : -0.08 (0.17), residues: 1356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 649 time to evaluate : 4.648 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 62 residues processed: 702 average time/residue: 1.3390 time to fit residues: 1209.0129 Evaluate side-chains 680 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 618 time to evaluate : 4.419 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 29 residues processed: 38 average time/residue: 1.1124 time to fit residues: 62.3348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 0.6980 chunk 302 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 191 optimal weight: 0.5980 chunk 270 optimal weight: 10.0000 chunk 403 optimal weight: 0.9990 chunk 427 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 382 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AE 20 GLN ** AI 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN BG 21 HIS ** BJ 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN M 188 ASN X 58 GLN ae 20 GLN af 52 ASN ** ag 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ai 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** aj 20 GLN ** aj 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** al 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bd 16 GLN bg 21 HIS ** bj 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 52 ASN m 188 ASN x 58 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 47562 Z= 0.176 Angle : 2.357 30.855 65208 Z= 0.799 Chirality : 0.037 0.197 6386 Planarity : 0.004 0.037 7950 Dihedral : 19.704 179.992 8276 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.66 (0.12), residues: 4532 helix: 2.46 (0.09), residues: 3010 sheet: 0.93 (0.69), residues: 44 loop : 0.38 (0.17), residues: 1478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 647 time to evaluate : 4.620 Fit side-chains outliers start: 110 outliers final: 33 residues processed: 699 average time/residue: 1.2900 time to fit residues: 1173.2956 Evaluate side-chains 647 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 614 time to evaluate : 4.602 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 23 residues processed: 10 average time/residue: 0.8386 time to fit residues: 18.0295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 318 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 364 optimal weight: 0.9980 chunk 295 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 383 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 20 GLN AE 20 GLN ** AI 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN BG 21 HIS H 52 ASN M 188 ASN ae 20 GLN af 52 ASN ** ai 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** aj 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ak 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** al 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bd 16 GLN bg 21 HIS h 52 ASN m 188 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 47562 Z= 0.342 Angle : 2.414 30.909 65208 Z= 0.826 Chirality : 0.043 0.240 6386 Planarity : 0.005 0.041 7950 Dihedral : 20.268 179.997 8276 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.03 (0.12), residues: 4532 helix: 1.98 (0.09), residues: 3036 sheet: 0.61 (0.69), residues: 44 loop : 0.07 (0.17), residues: 1452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 636 time to evaluate : 4.916 Fit side-chains outliers start: 127 outliers final: 54 residues processed: 697 average time/residue: 1.3739 time to fit residues: 1231.6883 Evaluate side-chains 675 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 621 time to evaluate : 4.637 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 32 residues processed: 22 average time/residue: 0.8016 time to fit residues: 31.2817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 0.3980 chunk 384 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 427 optimal weight: 6.9990 chunk 355 optimal weight: 1.9990 chunk 198 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AE 20 GLN AJ 20 GLN AJ 42 ASN ** AL 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN BG 21 HIS H 52 ASN M 188 ASN ae 20 GLN af 52 ASN ** ai 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** aj 42 ASN ** ak 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** al 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bd 16 GLN bg 21 HIS h 52 ASN m 188 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 47562 Z= 0.184 Angle : 2.306 30.534 65208 Z= 0.783 Chirality : 0.037 0.200 6386 Planarity : 0.004 0.040 7950 Dihedral : 19.692 179.998 8276 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.63 (0.12), residues: 4532 helix: 2.52 (0.09), residues: 2996 sheet: 0.78 (0.69), residues: 44 loop : 0.20 (0.17), residues: 1492 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 641 time to evaluate : 7.415 Fit side-chains outliers start: 102 outliers final: 44 residues processed: 697 average time/residue: 1.3575 time to fit residues: 1251.4280 Evaluate side-chains 657 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 613 time to evaluate : 4.533 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 33 residues processed: 11 average time/residue: 0.7971 time to fit residues: 18.9736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 0.7980 chunk 48 optimal weight: 0.0980 chunk 243 optimal weight: 5.9990 chunk 312 optimal weight: 4.9990 chunk 241 optimal weight: 0.9990 chunk 359 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 426 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 chunk 259 optimal weight: 6.9990 chunk 196 optimal weight: 0.5980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AE 20 GLN AJ 20 GLN AL 20 GLN BD 16 GLN BG 21 HIS H 52 ASN M 188 ASN aa 20 GLN ad 20 GLN ae 20 GLN af 52 ASN ah 20 GLN ** ai 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** aj 20 GLN ak 20 GLN al 20 GLN bd 16 GLN bg 21 HIS h 52 ASN m 188 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 47562 Z= 0.163 Angle : 2.255 28.080 65208 Z= 0.765 Chirality : 0.036 0.189 6386 Planarity : 0.004 0.037 7950 Dihedral : 19.357 179.991 8276 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.94 (0.12), residues: 4532 helix: 2.75 (0.09), residues: 2974 sheet: 0.99 (0.70), residues: 44 loop : 0.37 (0.17), residues: 1514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 650 time to evaluate : 4.763 Fit side-chains outliers start: 90 outliers final: 40 residues processed: 708 average time/residue: 1.2747 time to fit residues: 1170.0820 Evaluate side-chains 644 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 604 time to evaluate : 4.498 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 31 residues processed: 9 average time/residue: 0.8175 time to fit residues: 16.4915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 254 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 270 optimal weight: 10.0000 chunk 290 optimal weight: 0.6980 chunk 210 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 334 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 20 GLN AE 20 GLN ** AJ 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN BG 21 HIS H 52 ASN M 188 ASN X 18 ASN ** X 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ab 20 GLN ad 20 GLN ae 20 GLN ** ai 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** aj 20 GLN bd 16 GLN ** bg 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 52 ASN x 18 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 47562 Z= 0.370 Angle : 2.331 28.667 65208 Z= 0.801 Chirality : 0.045 0.240 6386 Planarity : 0.005 0.041 7950 Dihedral : 20.066 179.983 8276 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.82 (0.12), residues: 4532 helix: 1.81 (0.09), residues: 3123 sheet: 0.71 (0.70), residues: 44 loop : -0.11 (0.17), residues: 1365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 625 time to evaluate : 4.754 Fit side-chains outliers start: 92 outliers final: 44 residues processed: 684 average time/residue: 1.3544 time to fit residues: 1197.5206 Evaluate side-chains 650 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 606 time to evaluate : 4.504 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 32 residues processed: 12 average time/residue: 0.8338 time to fit residues: 20.3723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 0.8980 chunk 408 optimal weight: 0.9980 chunk 372 optimal weight: 1.9990 chunk 396 optimal weight: 0.0870 chunk 238 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 358 optimal weight: 0.9990 chunk 375 optimal weight: 0.2980 chunk 395 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 20 GLN AE 20 GLN AJ 20 GLN BD 16 GLN BG 21 HIS H 52 ASN M 188 ASN X 58 GLN ac 20 GLN ad 20 GLN ae 20 GLN ag 20 GLN aj 20 GLN bd 16 GLN bg 21 HIS h 52 ASN m 188 ASN x 58 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 47562 Z= 0.166 Angle : 2.217 26.909 65208 Z= 0.754 Chirality : 0.036 0.190 6386 Planarity : 0.004 0.039 7950 Dihedral : 19.451 179.996 8276 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.56 (0.12), residues: 4532 helix: 2.40 (0.09), residues: 3083 sheet: 0.99 (0.70), residues: 44 loop : 0.17 (0.17), residues: 1405 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 623 time to evaluate : 4.786 Fit side-chains outliers start: 60 outliers final: 37 residues processed: 662 average time/residue: 1.2883 time to fit residues: 1114.4014 Evaluate side-chains 637 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 600 time to evaluate : 4.685 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 34 residues processed: 4 average time/residue: 0.7381 time to fit residues: 10.2117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 10.0000 chunk 419 optimal weight: 5.9990 chunk 256 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 291 optimal weight: 0.8980 chunk 440 optimal weight: 0.8980 chunk 405 optimal weight: 0.3980 chunk 350 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 20 GLN AC 20 GLN AE 20 GLN ** AJ 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN ** BG 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN M 188 ASN X 18 ASN ab 20 GLN ** ac 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ae 20 GLN aj 20 GLN bd 16 GLN ** bg 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 52 ASN x 18 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 47562 Z= 0.304 Angle : 2.283 27.847 65208 Z= 0.783 Chirality : 0.042 0.221 6386 Planarity : 0.005 0.056 7950 Dihedral : 19.799 179.999 8276 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.26 (0.12), residues: 4532 helix: 2.25 (0.09), residues: 3008 sheet: 0.88 (0.73), residues: 42 loop : -0.03 (0.17), residues: 1482 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 623 time to evaluate : 4.785 Fit side-chains outliers start: 63 outliers final: 45 residues processed: 665 average time/residue: 1.3115 time to fit residues: 1131.4570 Evaluate side-chains 653 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 608 time to evaluate : 4.564 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 36 residues processed: 9 average time/residue: 0.7023 time to fit residues: 15.5274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 4.9990 chunk 373 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 323 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 351 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 360 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 20 GLN AE 20 GLN ** AJ 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN ** BG 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 ASN X 18 ASN ** X 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ae 20 GLN ** aj 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bd 16 GLN ** bg 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 188 ASN x 18 ASN ** x 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.153359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.114472 restraints weight = 49679.198| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.70 r_work: 0.2883 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.080 47562 Z= 0.359 Angle : 2.305 28.071 65208 Z= 0.793 Chirality : 0.045 0.233 6386 Planarity : 0.005 0.069 7950 Dihedral : 19.993 179.968 8276 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.78 (0.12), residues: 4532 helix: 1.88 (0.09), residues: 3024 sheet: 0.74 (0.68), residues: 44 loop : -0.22 (0.17), residues: 1464 =============================================================================== Job complete usr+sys time: 17881.66 seconds wall clock time: 315 minutes 41.31 seconds (18941.31 seconds total)