Starting phenix.real_space_refine (version: dev) on Thu Dec 22 02:34:34 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/12_2022/7vy2_32192_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/12_2022/7vy2_32192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/12_2022/7vy2_32192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/12_2022/7vy2_32192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/12_2022/7vy2_32192_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/12_2022/7vy2_32192_updated.pdb" } resolution = 2.75 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= 0.001 sd= 1.000 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 "L TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "K TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 229": "OE1" <-> "OE2" Residue "g TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "02 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "03 TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "06 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "07 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "08 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "08 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 46292 Number of models: 1 Model: "" Number of chains: 131 Chain: "L" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2233 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2437 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 293} Chain: "H" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1884 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 224} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 386 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "I" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 453 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 448 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'FME:plan-2': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "V" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 451 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "W" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "1" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "5" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "6" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 332 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "7" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 415 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "8" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "X" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 478 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "U" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 353 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "l" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2233 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "m" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2437 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 293} Chain: "h" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1884 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 224} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 386 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "d" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "i" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "k" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "o" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 453 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "q" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "s" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 454 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "v" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'FME:plan-2': 1, 'FME:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "w" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "y" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'FME:plan-2': 1, 'FME:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "z" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "01" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "02" 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: "03" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "04" 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: "05" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "06" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 332 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "07" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 415 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "08" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "x" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 456 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 54} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "u" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 71 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 12} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 482 Unusual residues: {'BCL': 2, 'BPH': 1, 'LMT': 2, 'PGV': 4, 'U10': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'PGV:plan-3': 3, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 51 Chain: "M" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 535 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CDL': 1, 'LMT': 4, 'PGV': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 185 Unusual residues: {'LMT': 1, 'PGV': 3, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 138 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'BCL': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'PGV': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 143 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 210 Unusual residues: {'BCL': 1, 'CDL': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 161 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Unusual residues: {'BCL': 1, 'CDL': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 6 Chain: "Z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "2" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SPO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "3" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 170 Unusual residues: {'BCL': 1, 'LMT': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "4" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 141 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "6" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 60 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Unusual residues: {'CDL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 9 Chain: "U" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {'LMT': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "l" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 345 Unusual residues: {'BCL': 1, 'BPH': 1, 'PGV': 4, 'U10': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'PGV:plan-3': 3, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 55 Chain: "m" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 634 Unusual residues: {' FE': 1, 'BCL': 3, 'BPH': 1, 'CDL': 2, 'LMT': 2, 'PGV': 2, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 2, 'CDL:plan-1': 1, 'U10:plan-10': 1} Unresolved non-hydrogen planarities: 12 Chain: "h" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 234 Unusual residues: {'CDL': 1, 'LMT': 2, 'PGV': 2, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 3 Chain: "b" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'BCL': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 27 Chain: "e" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 274 Unusual residues: {'BCL': 1, 'PGV': 2, 'PTY': 1, 'SPO': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "g" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 8 Chain: "j" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'BCL': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "n" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "o" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 166 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 205 Unusual residues: {'BCL': 1, 'LMT': 2, 'SPO': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 5 Chain: "t" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "w" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "y" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 211 Unusual residues: {'BCL': 1, 'CDL': 1, 'LDA': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "z" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "01" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "02" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "03" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 128 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "04" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "05" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "06" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "07" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "08" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'CDL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGV:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 24.45, per 1000 atoms: 0.53 Number of scatterers: 46292 At special positions: 0 Unit cell: (220.58, 163.18, 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 171 16.00 P 52 15.00 Mg 64 11.99 O 7184 8.00 N 6181 7.00 C 32638 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=60, symmetry=0 Number of additional bonds: simple=60, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.85 Conformation dependent library (CDL) restraints added in 5.5 seconds 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8434 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 10 sheets defined 65.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... 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 33 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 84 through 111 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.622A 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 162 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 226 through 247 removed outlier: 3.777A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 267 removed outlier: 3.670A pdb=" N TRP L 266 " --> pdb=" O TRP L 263 " (cutoff:3.500A) 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 Processing helix chain 'M' and resid 55 through 77 Processing helix chain 'M' and resid 82 through 87 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 139 Processing helix chain 'M' and resid 145 through 161 removed outlier: 3.792A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (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: 3.558A 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: 3.595A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 286 removed outlier: 3.911A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 301 Processing helix chain 'H' and resid 12 through 35 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 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: 3.828A pdb=" N PHE H 213 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 243 removed outlier: 3.628A pdb=" N GLY H 240 " --> pdb=" O TYR H 236 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 247 No H-bonds generated for 'chain 'H' and resid 245 through 247' Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 13 through 37 removed outlier: 4.226A pdb=" N VAL A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 44 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 13 through 37 removed outlier: 3.545A pdb=" N VAL D 18 " --> pdb=" O ARG D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'E' and resid 13 through 44 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 13 through 37 Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'G' and resid 13 through 44 removed outlier: 3.514A pdb=" N GLN G 17 " --> pdb=" O ASP G 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 13 through 37 Processing helix chain 'I' and resid 43 through 51 Processing helix chain 'J' and resid 13 through 44 Processing helix chain 'K' and resid 3 through 9 Processing helix chain 'K' and resid 13 through 37 Processing helix chain 'K' and resid 39 through 41 No H-bonds generated for 'chain 'K' and resid 39 through 41' Processing helix chain 'K' and resid 43 through 50 Processing helix chain 'N' and resid 13 through 44 Processing helix chain 'O' and resid 4 through 9 Processing helix chain 'O' and resid 13 through 37 Processing helix chain 'O' and resid 39 through 41 No H-bonds generated for 'chain 'O' and resid 39 through 41' Processing helix chain 'O' and resid 43 through 51 Processing helix chain 'P' and resid 15 through 44 Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 13 through 37 removed outlier: 3.521A pdb=" N VAL Q 18 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 50 Processing helix chain 'R' and resid 13 through 44 Processing helix chain 'S' and resid 4 through 9 Processing helix chain 'S' and resid 13 through 37 Processing helix chain 'S' and resid 43 through 50 Processing helix chain 'T' and resid 14 through 44 Processing helix chain 'V' and resid 4 through 10 Processing helix chain 'V' and resid 13 through 37 Processing helix chain 'V' and resid 43 through 50 Processing helix chain 'W' and resid 13 through 44 Processing helix chain 'Y' and resid 4 through 7 removed outlier: 3.540A pdb=" N ILE Y 7 " --> pdb=" O PHE Y 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 4 through 7' Processing helix chain 'Y' and resid 13 through 37 Processing helix chain 'Y' and resid 39 through 41 No H-bonds generated for 'chain 'Y' and resid 39 through 41' Processing helix chain 'Y' and resid 43 through 50 Processing helix chain 'Z' and resid 13 through 44 Processing helix chain '1' and resid 4 through 9 removed outlier: 3.814A pdb=" N TRP 1 8 " --> pdb=" O TYR 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 13 through 37 removed outlier: 3.680A pdb=" N VAL 1 18 " --> pdb=" O ARG 1 14 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 51 Processing helix chain '2' and resid 13 through 44 Processing helix chain '3' and resid 5 through 10 Processing helix chain '3' and resid 13 through 37 Processing helix chain '3' and resid 43 through 51 Processing helix chain '4' and resid 13 through 44 Processing helix chain '5' and resid 4 through 8 Processing helix chain '5' and resid 13 through 37 Processing helix chain '5' and resid 43 through 50 Processing helix chain '6' and resid 13 through 44 Processing helix chain '7' and resid 5 through 10 removed outlier: 3.776A pdb=" N TRP 7 8 " --> pdb=" O TYR 7 5 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE 7 10 " --> pdb=" O ILE 7 7 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 37 Processing helix chain '7' and resid 43 through 50 Processing helix chain '8' and resid 13 through 44 Processing helix chain 'X' and resid 15 through 53 Processing helix chain 'U' and resid 6 through 29 Processing helix chain 'U' and resid 32 through 48 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 33 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 84 through 111 Processing helix chain 'l' and resid 116 through 132 Processing helix chain 'l' and resid 134 through 138 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 153 through 164 removed outlier: 4.187A 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 226 through 249 removed outlier: 3.847A pdb=" N HIS l 230 " --> pdb=" O THR l 226 " (cutoff:3.500A) Processing helix chain 'l' and resid 259 through 267 removed outlier: 3.703A pdb=" N TRP l 265 " --> pdb=" O TRP l 262 " (cutoff:3.500A) Processing helix chain 'm' and resid 37 through 40 No H-bonds generated for 'chain 'm' and resid 37 through 40' Processing helix chain 'm' and resid 54 through 77 Processing helix chain 'm' and resid 82 through 87 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 139 Processing helix chain 'm' and resid 145 through 161 removed outlier: 3.665A pdb=" N ALA m 153 " --> pdb=" O ALA m 149 " (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: 3.741A 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 Processing helix chain 'm' and resid 264 through 286 removed outlier: 3.856A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) Processing helix chain 'm' and resid 294 through 301 Processing helix chain 'h' and resid 12 through 36 removed outlier: 3.596A pdb=" N MET h 36 " --> pdb=" O GLN h 32 " (cutoff:3.500A) 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 193 through 195 No H-bonds generated for 'chain 'h' and resid 193 through 195' Processing helix chain 'h' and resid 210 through 212 No H-bonds generated for 'chain 'h' and resid 210 through 212' Processing helix chain 'h' and resid 227 through 243 removed outlier: 3.916A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 9 Processing helix chain 'a' and resid 13 through 37 removed outlier: 4.597A pdb=" N VAL a 18 " --> pdb=" O ARG a 14 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 44 Processing helix chain 'd' and resid 3 through 9 Processing helix chain 'd' and resid 13 through 37 removed outlier: 4.241A pdb=" N VAL d 18 " --> pdb=" O ARG d 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 43 through 50 Processing helix chain 'e' and resid 13 through 44 Processing helix chain 'f' and resid 3 through 9 Processing helix chain 'f' and resid 13 through 37 Processing helix chain 'f' and resid 43 through 50 Processing helix chain 'g' and resid 13 through 44 Processing helix chain 'i' and resid 5 through 9 Processing helix chain 'i' and resid 13 through 37 Processing helix chain 'i' and resid 43 through 51 Processing helix chain 'j' and resid 13 through 44 Processing helix chain 'k' and resid 3 through 9 Processing helix chain 'k' and resid 13 through 37 Processing helix chain 'k' and resid 43 through 50 Processing helix chain 'n' and resid 13 through 44 Processing helix chain 'o' and resid 3 through 10 Processing helix chain 'o' and resid 13 through 37 Processing helix chain 'o' and resid 43 through 50 Processing helix chain 'p' and resid 15 through 44 Processing helix chain 'q' and resid 5 through 9 Processing helix chain 'q' and resid 13 through 37 Processing helix chain 'q' and resid 43 through 50 Processing helix chain 'r' and resid 13 through 44 Processing helix chain 's' and resid 5 through 9 Processing helix chain 's' and resid 13 through 37 Processing helix chain 's' and resid 43 through 50 Processing helix chain 't' and resid 13 through 44 Processing helix chain 'v' and resid 4 through 9 removed outlier: 3.842A pdb=" N ILE v 7 " --> pdb=" O PHE v 4 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP v 8 " --> pdb=" O TYR v 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 13 through 37 Processing helix chain 'v' and resid 43 through 50 Processing helix chain 'w' and resid 13 through 44 removed outlier: 4.213A pdb=" N VAL w 22 " --> pdb=" O GLU w 18 " (cutoff:3.500A) Processing helix chain 'y' and resid 3 through 10 removed outlier: 3.813A pdb=" N LYS y 6 " --> pdb=" O LYS y 3 " (cutoff:3.500A) Processing helix chain 'y' and resid 13 through 37 Processing helix chain 'y' and resid 43 through 50 Processing helix chain 'z' and resid 13 through 44 Processing helix chain '01' and resid 4 through 9 Processing helix chain '01' and resid 13 through 37 Processing helix chain '01' and resid 43 through 50 Processing helix chain '02' and resid 13 through 44 removed outlier: 3.531A pdb=" N LEU02 29 " --> pdb=" O SER02 25 " (cutoff:3.500A) Processing helix chain '03' and resid 4 through 10 Processing helix chain '03' and resid 13 through 37 Processing helix chain '03' and resid 43 through 51 Processing helix chain '04' and resid 13 through 44 Processing helix chain '05' and resid 4 through 9 Processing helix chain '05' and resid 13 through 37 Processing helix chain '05' and resid 43 through 51 Processing helix chain '06' and resid 13 through 44 Processing helix chain '07' and resid 5 through 10 removed outlier: 3.887A pdb=" N TRP07 8 " --> pdb=" O TYR07 5 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE07 10 " --> pdb=" O ILE07 7 " (cutoff:3.500A) Processing helix chain '07' and resid 13 through 37 Processing helix chain '07' and resid 43 through 51 Processing helix chain '08' and resid 13 through 44 Processing helix chain 'x' and resid 15 through 54 removed outlier: 3.502A pdb=" N ARG x 20 " --> pdb=" O LYS x 16 " (cutoff:3.500A) Processing helix chain 'u' and resid 56 through 60 Processing sheet with id= A, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.641A pdb=" N PHE L 24 " --> pdb=" O VAL L 31 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 62 through 65 Processing sheet with id= C, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= D, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.646A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 196 through 198 removed outlier: 7.496A pdb=" N VAL H 205 " --> pdb=" O PRO H 152 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG H 154 " --> pdb=" O VAL H 205 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'l' and resid 24 through 26 removed outlier: 3.681A pdb=" N PHE l 24 " --> pdb=" O VAL l 31 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'h' and resid 62 through 65 Processing sheet with id= H, first strand: chain 'h' and resid 87 through 89 Processing sheet with id= I, first strand: chain 'h' and resid 131 through 133 removed outlier: 6.788A pdb=" N GLU h 180 " --> pdb=" O VAL h 165 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE h 167 " --> pdb=" O PHE h 178 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE h 178 " --> pdb=" O ILE h 167 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'h' and resid 202 through 204 removed outlier: 3.774A pdb=" N GLY h 162 " --> pdb=" O VAL h 153 " (cutoff:3.500A) 2241 hydrogen bonds defined for protein. 6432 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: 16.41 Time building geometry restraints manager: 22.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 13568 1.37 - 1.54: 33452 1.54 - 1.71: 384 1.71 - 1.88: 332 1.88 - 2.05: 256 Bond restraints: 47992 Sorted by residual: bond pdb=" CA7 CDL m 410 " pdb=" OA8 CDL m 410 " ideal model delta sigma weight residual 1.334 1.458 -0.124 1.10e-02 8.26e+03 1.28e+02 bond pdb=" CA7 CDL y 102 " pdb=" OA8 CDL y 102 " ideal model delta sigma weight residual 1.334 1.458 -0.124 1.10e-02 8.26e+03 1.27e+02 bond pdb=" CA7 CDL h 805 " pdb=" OA8 CDL h 805 " ideal model delta sigma weight residual 1.334 1.457 -0.123 1.10e-02 8.26e+03 1.26e+02 bond pdb=" CA7 CDL X 101 " pdb=" OA8 CDL X 101 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" CA7 CDL K 401 " pdb=" OA8 CDL K 401 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.22e+02 ... (remaining 47987 not shown) Histogram of bond angle deviations from ideal: 83.17 - 102.38: 844 102.38 - 121.58: 54369 121.58 - 140.79: 10206 140.79 - 160.00: 74 160.00 - 179.20: 122 Bond angle restraints: 65615 Sorted by residual: angle pdb=" C1D BCL f 102 " pdb=" C2D BCL f 102 " pdb=" CMD BCL f 102 " ideal model delta sigma weight residual 125.57 140.61 -15.04 1.83e+00 2.99e-01 6.77e+01 angle pdb=" C1D BCL a 101 " pdb=" C2D BCL a 101 " pdb=" CMD BCL a 101 " ideal model delta sigma weight residual 125.57 140.05 -14.48 1.83e+00 2.99e-01 6.27e+01 angle pdb=" C1D BCL d 101 " pdb=" C2D BCL d 101 " pdb=" CMD BCL d 101 " ideal model delta sigma weight residual 125.57 139.82 -14.24 1.83e+00 2.99e-01 6.07e+01 angle pdb=" C1D BCL b 101 " pdb=" C2D BCL b 101 " pdb=" CMD BCL b 101 " ideal model delta sigma weight residual 125.57 139.76 -14.19 1.83e+00 2.99e-01 6.02e+01 angle pdb=" C1D BCL o 101 " pdb=" C2D BCL o 101 " pdb=" CMD BCL o 101 " ideal model delta sigma weight residual 125.57 139.76 -14.19 1.83e+00 2.99e-01 6.02e+01 ... (remaining 65610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 23940 35.98 - 71.96: 1038 71.96 - 107.94: 83 107.94 - 143.92: 22 143.92 - 179.89: 13 Dihedral angle restraints: 25096 sinusoidal: 11979 harmonic: 13117 Sorted by residual: dihedral pdb=" C1 BCL a 101 " pdb=" CGA BCL a 101 " pdb=" O2A BCL a 101 " pdb=" CBA BCL a 101 " ideal model delta sinusoidal sigma weight residual 180.00 73.33 106.67 1 6.00e+00 2.78e-02 3.43e+02 dihedral pdb=" C1 BCL M 401 " pdb=" C2 BCL M 401 " pdb=" C3 BCL M 401 " pdb=" C5 BCL M 401 " ideal model delta sinusoidal sigma weight residual -180.00 -0.29 -179.71 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL m 402 " pdb=" C2 BCL m 402 " pdb=" C3 BCL m 402 " pdb=" C5 BCL m 402 " ideal model delta sinusoidal sigma weight residual -180.00 -0.94 -179.06 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 25093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 5761 0.088 - 0.177: 560 0.177 - 0.265: 120 0.265 - 0.353: 24 0.353 - 0.442: 2 Chirality restraints: 6467 Sorted by residual: chirality pdb=" C4' LMT h 803 " pdb=" C3' LMT h 803 " pdb=" C5' LMT h 803 " pdb=" O1B LMT h 803 " both_signs ideal model delta sigma weight residual False -2.76 -2.32 -0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" C4' LMT 5 101 " pdb=" C3' LMT 5 101 " pdb=" C5' LMT 5 101 " pdb=" O1B LMT 5 101 " both_signs ideal model delta sigma weight residual False -2.76 -2.40 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C4' LMT03 101 " pdb=" C3' LMT03 101 " pdb=" C5' LMT03 101 " pdb=" O1B LMT03 101 " both_signs ideal model delta sigma weight residual False -2.76 -2.41 -0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 6464 not shown) Planarity restraints: 7851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL Z 101 " 0.371 3.00e-02 1.11e+03 3.06e-01 5.21e+02 pdb=" CBA BCL Z 101 " 0.157 3.00e-02 1.11e+03 pdb=" CGA BCL Z 101 " -0.083 3.00e-02 1.11e+03 pdb=" O1A BCL Z 101 " 0.094 3.00e-02 1.11e+03 pdb=" O2A BCL Z 101 " -0.539 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL a 101 " -0.347 3.00e-02 1.11e+03 2.92e-01 4.73e+02 pdb=" CBA BCL a 101 " -0.033 3.00e-02 1.11e+03 pdb=" CGA BCL a 101 " 0.062 3.00e-02 1.11e+03 pdb=" O1A BCL a 101 " -0.195 3.00e-02 1.11e+03 pdb=" O2A BCL a 101 " 0.512 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BCL 7 101 " -0.230 3.10e-02 1.04e+03 2.86e-01 4.27e+02 pdb=" C4C BCL 7 101 " -0.199 3.10e-02 1.04e+03 pdb=" CHC BCL 7 101 " -0.056 3.10e-02 1.04e+03 pdb=" CHD BCL 7 101 " -0.071 3.10e-02 1.04e+03 pdb=" NC BCL 7 101 " 0.556 3.10e-02 1.04e+03 ... (remaining 7848 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 298 2.53 - 3.13: 33115 3.13 - 3.72: 77205 3.72 - 4.31: 114144 4.31 - 4.90: 183351 Nonbonded interactions: 408113 Sorted by model distance: nonbonded pdb=" OE2 GLU m 234 " pdb="FE FE m 405 " model vdw 1.943 2.260 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 404 " model vdw 1.964 2.260 nonbonded pdb=" CE1 HIS e 38 " pdb="MG BCL e 102 " model vdw 1.989 3.130 nonbonded pdb=" O ALA L 78 " pdb=" O3' LMT L 305 " model vdw 2.026 2.440 nonbonded pdb=" CE1 HIS E 38 " pdb="MG BCL E 101 " model vdw 2.103 3.130 ... (remaining 408108 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 '01' and ((resid 4 through 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain '03' and ((resid 4 through 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain '05' and ((resid 4 through 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain '07' and (resid 4 through 10 or (resid 11 and (name N or name CA or name \ C or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or nam \ e CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain '1' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain '3' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain '5' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain '7' and (resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 54)) selection = (chain 'F' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'I' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'K' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'O' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'Q' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'S' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 53 or (resid 54 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'V' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 53 or (resid 54 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'Y' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'd' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 54)) selection = (chain 'f' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'i' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'k' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'o' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'q' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 's' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'v' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'y' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain '02' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or nam \ e CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '04' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or nam \ e CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '06' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or nam \ e CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '08' and resid 11 through 48) selection = (chain '2' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '4' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '6' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '8' and resid 11 through 48) selection = (chain 'B' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'E' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'G' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'J' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'N' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'P' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'R' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'T' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'W' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'Z' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'b' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'e' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'g' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'j' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'n' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'p' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'r' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 't' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'w' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'z' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) } ncs_group { reference = (chain 'A' and resid 1 through 45) selection = (chain 'a' and resid 1 through 45) } ncs_group { reference = (chain 'H' and (resid 1 through 248 or resid 801 or (resid 802 and (name C1 or n \ ame C1' or name C10 or name C11 or name C12 or name C1B or name C2 or name C2' o \ r name C2B or name C3 or name C3' or name C4 or name C4' or name C5 or name C5' \ or name C6 or name C6' or name C7 or name C8 or name C9 or name O1' or name O1B \ or name O2' or name O3' or name O5' or name O5B or name O6')))) selection = (chain 'h' and (resid 1 through 248 or resid 801 through 802)) } ncs_group { reference = (chain 'L' and (resid 1 through 281 or resid 301 through 304 or (resid 307 and ( \ name C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C1 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C \ 3 or name C4 or name C5 or name C6 or name C7 or name C8 or name O01 or name O02 \ or name O03 or name O04 or name O05 or name O06 or name O11 or name O12 or name \ O13 or name O14 or name P )) or (resid 308 and (name C01 or name C02 or name C0 \ 3 or name C04 or name C05 or name C06 or name C1 or name C19 or name C2 or name \ C20 or name C21 or name C3 or name C4 or name O01 or name O02 or name O03 or nam \ e O04 or name O05 or name O06 or name O11 or name O12 or name O13 or name O14 or \ name P )))) selection = (chain 'l' and (resid 1 through 281 or resid 301 through 304 or resid 307 throug \ h 308)) } ncs_group { reference = (chain 'M' and (resid 1 through 306 or resid 401 through 402 or resid 408 throug \ h 411)) selection = (chain 'm' and (resid 1 through 306 or resid 401 through 402 or (resid 408 and ( \ name C1 or name C1' or name C10 or name C11 or name C12 or name C1B or name C2 o \ r name C2' or name C3 or name C3' or name C4 or name C4' or name C5 or name C5' \ or name C6 or name C6' or name C7 or name C8 or name C9 or name O1' or name O1B \ or name O2' or name O3' or name O5' or name O6')) or resid 409 through 411)) } ncs_group { reference = (chain 'X' and (resid 10 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 69 or (resid 102 and (name CB2 or \ name OB2 or name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name CA2 or name CA3 or name CA4 or name \ CA5 or name O1 or name OA2 or name OA3 or name OA4 or name OA5 or name OA6 or na \ me OA7 or name OB4 or name OB5 or name PA1 or name PB2)))) selection = (chain 'x' and (resid 10 through 69 or resid 102)) } 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 52 5.49 5 Mg 64 5.21 5 S 171 5.16 5 C 32638 2.51 5 N 6181 2.21 5 O 7184 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: 3.630 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: 0.030 Extract box with map and model: 23.550 Check model and map are aligned: 0.680 Convert atoms to be neutral: 0.420 Process input model: 112.550 Find NCS groups from input model: 4.080 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.050 Load rotamer database and sin/cos tables:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.020 0.183 47992 Z= 1.002 Angle : 1.907 18.686 65615 Z= 0.829 Chirality : 0.061 0.442 6467 Planarity : 0.018 0.306 7851 Dihedral : 18.896 179.895 16662 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 3.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.62 (0.12), residues: 4376 helix: 1.75 (0.09), residues: 2932 sheet: -0.67 (0.65), residues: 62 loop : -0.25 (0.17), residues: 1382 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 916 time to evaluate : 4.715 Fit side-chains outliers start: 126 outliers final: 48 residues processed: 991 average time/residue: 1.1167 time to fit residues: 1472.2063 Evaluate side-chains 800 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 752 time to evaluate : 4.654 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 33 residues processed: 15 average time/residue: 0.9162 time to fit residues: 24.6778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 0.9990 chunk 325 optimal weight: 0.5980 chunk 180 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 336 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 204 optimal weight: 20.0000 chunk 250 optimal weight: 0.9990 chunk 389 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 183 ASN M 301 HIS H 52 ASN H 126 HIS A 20 GLN A 42 ASN B 17 GLN E 38 HIS F 20 GLN G 15 GLN G 17 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN W 17 GLN 2 15 GLN 5 20 GLN 6 15 GLN ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 20 GLN X 66 ASN l 199 ASN m 259 ASN ** m 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 199 GLN ** h 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 HIS ** e 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN ** r 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 HIS v 20 GLN w 15 GLN w 17 GLN y 52 ASN 01 20 GLN 01 42 ASN 02 17 GLN 04 17 GLN 04 20 HIS x 60 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 47992 Z= 0.172 Angle : 0.717 14.754 65615 Z= 0.278 Chirality : 0.038 0.290 6467 Planarity : 0.003 0.048 7851 Dihedral : 18.215 179.279 8867 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 4.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.13), residues: 4376 helix: 1.99 (0.09), residues: 2932 sheet: -0.13 (0.75), residues: 46 loop : -0.11 (0.18), residues: 1398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 827 time to evaluate : 4.756 Fit side-chains outliers start: 165 outliers final: 61 residues processed: 913 average time/residue: 1.0969 time to fit residues: 1345.8622 Evaluate side-chains 804 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 743 time to evaluate : 4.398 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 44 residues processed: 19 average time/residue: 0.5937 time to fit residues: 24.2968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 324 optimal weight: 2.9990 chunk 265 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 390 optimal weight: 4.9990 chunk 421 optimal weight: 20.0000 chunk 347 optimal weight: 9.9990 chunk 387 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 313 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 GLN A 20 GLN F 20 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN ** O 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN R 20 HIS T 15 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 60 ASN l 20 ASN m 81 ASN m 301 HIS a 20 GLN ** d 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN q 20 GLN ** r 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 20 GLN 01 42 ASN 04 20 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 47992 Z= 0.348 Angle : 0.804 16.471 65615 Z= 0.323 Chirality : 0.042 0.180 6467 Planarity : 0.004 0.061 7851 Dihedral : 18.416 179.684 8867 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 4.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.55 (0.12), residues: 4376 helix: 1.68 (0.09), residues: 2947 sheet: -0.26 (0.74), residues: 46 loop : -0.27 (0.17), residues: 1383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 775 time to evaluate : 4.573 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 182 outliers final: 94 residues processed: 870 average time/residue: 1.0942 time to fit residues: 1278.6899 Evaluate side-chains 826 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 732 time to evaluate : 4.523 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 58 residues processed: 38 average time/residue: 0.6034 time to fit residues: 42.1360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 186 optimal weight: 20.0000 chunk 262 optimal weight: 0.8980 chunk 391 optimal weight: 3.9990 chunk 414 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 371 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** O 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** d 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN q 20 GLN v 20 GLN y 52 ASN 01 20 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 47992 Z= 0.208 Angle : 0.706 14.879 65615 Z= 0.282 Chirality : 0.038 0.174 6467 Planarity : 0.003 0.061 7851 Dihedral : 17.717 179.820 8867 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 4.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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 (0.13), residues: 4376 helix: 1.86 (0.09), residues: 2953 sheet: -0.18 (0.75), residues: 46 loop : -0.20 (0.18), residues: 1377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 783 time to evaluate : 4.762 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 185 outliers final: 88 residues processed: 894 average time/residue: 1.0625 time to fit residues: 1281.1164 Evaluate side-chains 825 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 737 time to evaluate : 4.664 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 61 residues processed: 27 average time/residue: 0.6061 time to fit residues: 31.7764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 308 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 353 optimal weight: 2.9990 chunk 286 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 372 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN h 52 ASN ** d 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN ** r 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 20 GLN y 52 ASN 01 42 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 47992 Z= 0.198 Angle : 0.695 15.611 65615 Z= 0.279 Chirality : 0.038 0.197 6467 Planarity : 0.003 0.068 7851 Dihedral : 17.302 179.794 8867 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 4.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.90 (0.13), residues: 4376 helix: 1.81 (0.09), residues: 3027 sheet: -0.16 (0.75), residues: 46 loop : 0.10 (0.18), residues: 1303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 782 time to evaluate : 4.791 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 185 outliers final: 87 residues processed: 893 average time/residue: 1.0729 time to fit residues: 1297.1276 Evaluate side-chains 825 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 738 time to evaluate : 4.641 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 64 residues processed: 24 average time/residue: 0.7055 time to fit residues: 31.3666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 5.9990 chunk 373 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 243 optimal weight: 0.0060 chunk 102 optimal weight: 0.9990 chunk 415 optimal weight: 7.9990 chunk 344 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 217 optimal weight: 0.2980 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** O 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN R 17 GLN T 15 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN ** r 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 20 GLN y 52 ASN 01 42 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 47992 Z= 0.187 Angle : 0.685 15.586 65615 Z= 0.277 Chirality : 0.038 0.266 6467 Planarity : 0.003 0.053 7851 Dihedral : 16.894 179.789 8867 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 4.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.12), residues: 4376 helix: 2.17 (0.09), residues: 2895 sheet: -0.12 (0.76), residues: 46 loop : 0.26 (0.17), residues: 1435 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 776 time to evaluate : 5.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 180 outliers final: 93 residues processed: 876 average time/residue: 1.1401 time to fit residues: 1358.7224 Evaluate side-chains 824 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 731 time to evaluate : 4.756 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 65 residues processed: 30 average time/residue: 0.7148 time to fit residues: 39.6676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 chunk 349 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 413 optimal weight: 20.0000 chunk 258 optimal weight: 0.7980 chunk 252 optimal weight: 5.9990 chunk 190 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 56 GLN ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 81 ASN a 20 GLN ** d 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN ** r 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 20 GLN y 52 ASN 01 42 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.080 47992 Z= 0.432 Angle : 0.875 17.453 65615 Z= 0.356 Chirality : 0.045 0.324 6467 Planarity : 0.005 0.070 7851 Dihedral : 18.117 179.919 8867 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 5.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.12), residues: 4376 helix: 1.61 (0.09), residues: 2897 sheet: -0.52 (0.71), residues: 46 loop : 0.02 (0.17), residues: 1433 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 754 time to evaluate : 4.792 Fit side-chains outliers start: 190 outliers final: 104 residues processed: 865 average time/residue: 1.1031 time to fit residues: 1282.0934 Evaluate side-chains 829 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 725 time to evaluate : 4.667 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 74 residues processed: 32 average time/residue: 0.4864 time to fit residues: 32.9302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 262 optimal weight: 0.8980 chunk 281 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 325 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN R 17 GLN T 15 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN l 56 GLN ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** d 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 15 GLN v 20 GLN y 52 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 47992 Z= 0.181 Angle : 0.708 15.177 65615 Z= 0.289 Chirality : 0.038 0.244 6467 Planarity : 0.003 0.066 7851 Dihedral : 17.157 179.806 8867 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 3.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.12), residues: 4376 helix: 2.01 (0.09), residues: 2891 sheet: -0.33 (0.75), residues: 46 loop : 0.16 (0.17), residues: 1439 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 768 time to evaluate : 5.015 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 83 residues processed: 856 average time/residue: 1.0742 time to fit residues: 1248.6414 Evaluate side-chains 817 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 734 time to evaluate : 4.484 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 67 residues processed: 19 average time/residue: 0.7062 time to fit residues: 25.9102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 9.9990 chunk 396 optimal weight: 5.9990 chunk 361 optimal weight: 1.9990 chunk 385 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 167 optimal weight: 0.2980 chunk 302 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 348 optimal weight: 5.9990 chunk 364 optimal weight: 6.9990 chunk 383 optimal weight: 10.0000 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN ** O 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 15 GLN ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** d 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN r 15 GLN v 20 GLN y 52 ASN 01 42 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 47992 Z= 0.343 Angle : 0.822 16.056 65615 Z= 0.337 Chirality : 0.043 0.306 6467 Planarity : 0.004 0.069 7851 Dihedral : 17.775 179.797 8867 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 3.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.67 (0.12), residues: 4376 helix: 1.71 (0.09), residues: 2889 sheet: -0.42 (0.73), residues: 46 loop : 0.03 (0.17), residues: 1441 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 734 time to evaluate : 5.035 Fit side-chains outliers start: 134 outliers final: 86 residues processed: 820 average time/residue: 1.0958 time to fit residues: 1213.5189 Evaluate side-chains 794 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 708 time to evaluate : 4.512 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 71 residues processed: 16 average time/residue: 0.7172 time to fit residues: 23.4221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 2.9990 chunk 407 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 283 optimal weight: 4.9990 chunk 427 optimal weight: 3.9990 chunk 393 optimal weight: 9.9990 chunk 340 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 262 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 GLN K 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** d 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 15 GLN v 20 GLN y 52 ASN 01 42 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 47992 Z= 0.323 Angle : 0.814 16.067 65615 Z= 0.336 Chirality : 0.043 0.341 6467 Planarity : 0.004 0.065 7851 Dihedral : 17.732 179.844 8867 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.55 (0.12), residues: 4376 helix: 1.62 (0.09), residues: 2889 sheet: -0.45 (0.74), residues: 46 loop : -0.03 (0.17), residues: 1441 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 723 time to evaluate : 4.974 Fit side-chains outliers start: 108 outliers final: 88 residues processed: 803 average time/residue: 1.0923 time to fit residues: 1185.1125 Evaluate side-chains 791 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 703 time to evaluate : 4.676 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 75 residues processed: 17 average time/residue: 0.7390 time to fit residues: 24.7386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 0.9980 chunk 362 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 313 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 340 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 350 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 62 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN R 17 GLN T 15 GLN ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN m 4 GLN d 20 GLN ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 20 HIS v 20 GLN y 52 ASN 01 42 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.167340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.133473 restraints weight = 69242.966| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.47 r_work: 0.3331 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 47992 Z= 0.172 Angle : 0.704 15.071 65615 Z= 0.290 Chirality : 0.038 0.267 6467 Planarity : 0.003 0.055 7851 Dihedral : 16.761 179.822 8867 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 2.04 (0.12), residues: 4376 helix: 1.99 (0.09), residues: 2904 sheet: -0.23 (0.77), residues: 46 loop : 0.15 (0.17), residues: 1426 =============================================================================== Job complete usr+sys time: 18251.81 seconds wall clock time: 322 minutes 9.21 seconds (19329.21 seconds total)