Starting phenix.real_space_refine (version: dev) on Wed Dec 21 07:36:28 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7va9_31835/12_2022/7va9_31835_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7va9_31835/12_2022/7va9_31835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7va9_31835/12_2022/7va9_31835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7va9_31835/12_2022/7va9_31835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7va9_31835/12_2022/7va9_31835_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7va9_31835/12_2022/7va9_31835_updated.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 GLU 104": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L ARG 109": "NH1" <-> "NH2" Residue "L TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 217": "NH1" <-> "NH2" Residue "L ARG 231": "NH1" <-> "NH2" Residue "M ARG 87": "NH1" <-> "NH2" Residue "M GLU 95": "OE1" <-> "OE2" Residue "M ARG 136": "NH1" <-> "NH2" Residue "M ASP 184": "OD1" <-> "OD2" Residue "M ARG 253": "NH1" <-> "NH2" Residue "H PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 46": "OD1" <-> "OD2" Residue "H ARG 89": "NH1" <-> "NH2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H ASP 107": "OD1" <-> "OD2" Residue "H ARG 118": "NH1" <-> "NH2" Residue "H TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "B TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "F TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 14": "NH1" <-> "NH2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "I ARG 14": "NH1" <-> "NH2" Residue "I PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 45": "OE1" <-> "OE2" Residue "I ARG 53": "NH1" <-> "NH2" Residue "K ARG 14": "NH1" <-> "NH2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "O ARG 14": "NH1" <-> "NH2" Residue "O ARG 53": "NH1" <-> "NH2" Residue "Q ARG 14": "NH1" <-> "NH2" Residue "Q ARG 53": "NH1" <-> "NH2" Residue "S ARG 14": "NH1" <-> "NH2" Residue "S TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 53": "NH1" <-> "NH2" Residue "U ARG 15": "NH1" <-> "NH2" Residue "U ARG 53": "NH1" <-> "NH2" Residue "W ARG 15": "NH1" <-> "NH2" Residue "W ARG 53": "NH1" <-> "NH2" Residue "Y ARG 15": "NH1" <-> "NH2" Residue "Y ARG 53": "NH1" <-> "NH2" Residue "1 ARG 15": "NH1" <-> "NH2" Residue "1 ARG 53": "NH1" <-> "NH2" Residue "2 ARG 46": "NH1" <-> "NH2" Residue "7 TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 12": "OD1" <-> "OD2" Residue "7 ARG 14": "NH1" <-> "NH2" Residue "9 ARG 14": "NH1" <-> "NH2" Residue "9 ARG 53": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "l GLU 104": "OE1" <-> "OE2" Residue "l GLU 106": "OE1" <-> "OE2" Residue "l ARG 109": "NH1" <-> "NH2" Residue "l TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 217": "NH1" <-> "NH2" Residue "l ARG 231": "NH1" <-> "NH2" Residue "m ARG 87": "NH1" <-> "NH2" Residue "m GLU 95": "OE1" <-> "OE2" Residue "m ARG 136": "NH1" <-> "NH2" Residue "m ASP 184": "OD1" <-> "OD2" Residue "m ARG 253": "NH1" <-> "NH2" Residue "h PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 46": "OD1" <-> "OD2" Residue "h ARG 89": "NH1" <-> "NH2" Residue "h GLU 94": "OE1" <-> "OE2" Residue "h ASP 107": "OD1" <-> "OD2" Residue "h ARG 118": "NH1" <-> "NH2" Residue "h TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 12": "OD1" <-> "OD2" Residue "a ARG 14": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 53": "NH1" <-> "NH2" Residue "f TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 12": "OD1" <-> "OD2" Residue "f ARG 14": "NH1" <-> "NH2" Residue "f ARG 53": "NH1" <-> "NH2" Residue "i ARG 14": "NH1" <-> "NH2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "k ARG 14": "NH1" <-> "NH2" Residue "k ARG 53": "NH1" <-> "NH2" Residue "o ARG 14": "NH1" <-> "NH2" Residue "o ARG 53": "NH1" <-> "NH2" Residue "q ARG 14": "NH1" <-> "NH2" Residue "q ARG 53": "NH1" <-> "NH2" Residue "s ARG 14": "NH1" <-> "NH2" Residue "s TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 53": "NH1" <-> "NH2" Residue "u ARG 15": "NH1" <-> "NH2" Residue "u ARG 53": "NH1" <-> "NH2" Residue "v TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 15": "NH1" <-> "NH2" Residue "w ARG 53": "NH1" <-> "NH2" Residue "y ARG 15": "NH1" <-> "NH2" Residue "y ARG 53": "NH1" <-> "NH2" Residue "5 ARG 15": "NH1" <-> "NH2" Residue "5 ARG 53": "NH1" <-> "NH2" Residue "4 ARG 46": "NH1" <-> "NH2" Residue "6 ARG 14": "NH1" <-> "NH2" Residue "6 GLU 45": "OE1" <-> "OE2" Residue "3 ARG 14": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "c ARG 49": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 42176 Number of models: 1 Model: "" Number of chains: 124 Chain: "L" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2431 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "H" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1972 Classifications: {'peptide': 260} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 236} Chain: "A" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "G" 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: "I" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "N" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 316 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "O" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "P" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 316 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "Q" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "R" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 316 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "S" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "T" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 316 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "U" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 362 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "V" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "W" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "X" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "Y" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "Z" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "1" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "2" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 297 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "7" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 392 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "8" 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: "9" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "0" 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: "C" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 507 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "l" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "m" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2431 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "h" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1972 Classifications: {'peptide': 260} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 236} Chain: "a" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "g" 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: "i" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "n" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "o" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "p" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "q" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "r" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "s" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "t" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "u" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 362 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "v" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "w" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "x" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "y" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "z" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "5" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "4" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 297 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "6" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 392 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "aa" 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: "3" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "ab" 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: "c" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 507 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "L" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 335 Unusual residues: {'BCL': 2, 'BPB': 2, 'PC1': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 16 Chain: "M" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 376 Unusual residues: {'BCL': 2, 'CDL': 1, 'FE2': 1, 'PC1': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 205 Unusual residues: {'BCL': 1, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 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: 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: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "F" 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: "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: 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: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 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: "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: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'SPO:plan-4': 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'SPO:plan-4': 1} Unresolved non-hydrogen planarities: 4 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: "U" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 154 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "W" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "X" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "Y" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "Z" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "1" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "2" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "7" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" 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: "9" 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: "0" 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: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 360 Unusual residues: {'BCL': 2, 'BPB': 2, 'PC1': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 323 Unusual residues: {'BCL': 2, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "h" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "a" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 197 Unusual residues: {'BCL': 1, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 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: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "e" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'SPO:plan-4': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "g" 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: "i" 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: "j" 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: "k" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 164 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'SPO:plan-4': 1, 'SPO:plan-3': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "q" 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: "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: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 238 Unusual residues: {'BCL': 2, 'SPO': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "t" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "x" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "y" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "z" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "5" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "aa" 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: "3" 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: "ab" 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: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 22.03, per 1000 atoms: 0.52 Number of scatterers: 42176 At special positions: 0 Unit cell: (226.18, 136.702, 126.76, 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 162 16.00 P 15 15.00 Mg 64 11.99 O 6362 8.00 N 5997 7.00 C 29574 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=56, symmetry=0 Number of additional bonds: simple=56, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.04 Conformation dependent library (CDL) restraints added in 5.4 seconds 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8136 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 181 helices and 8 sheets defined 66.3% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 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 32 through 56 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 84 through 111 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.521A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 152 through 164 removed outlier: 4.044A 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 219 Processing helix chain 'L' and resid 226 through 249 Processing helix chain 'L' and resid 259 through 267 removed outlier: 4.400A pdb=" N TRP L 265 " --> pdb=" O ASP L 261 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 41 removed outlier: 3.579A pdb=" N TRP M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 37 through 41' Processing helix chain 'M' and resid 54 through 78 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 Processing helix chain 'M' and resid 163 through 168 Processing helix chain 'M' and resid 171 through 173 No H-bonds generated for 'chain 'M' and resid 171 through 173' Processing helix chain 'M' and resid 179 through 192 Processing helix chain 'M' and resid 196 through 198 No H-bonds generated for 'chain 'M' and resid 196 through 198' Processing helix chain 'M' and resid 200 through 229 removed outlier: 4.919A pdb=" N ARG M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N PHE M 229 " --> pdb=" O ALA M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 256 Processing helix chain 'M' and resid 264 through 286 removed outlier: 3.984A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 300 Processing helix chain 'H' and resid 12 through 36 Processing helix chain 'H' and resid 104 through 107 No H-bonds generated for 'chain 'H' and resid 104 through 107' Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 210 through 213 No H-bonds generated for 'chain 'H' and resid 210 through 213' Processing helix chain 'H' and resid 227 through 243 removed outlier: 4.195A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 259 Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 13 through 37 Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'B' and resid 14 through 45 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 13 through 37 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'E' and resid 14 through 45 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 14 through 45 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 50 Processing helix chain 'J' and resid 14 through 45 Processing helix chain 'K' and resid 4 through 9 Processing helix chain 'K' and resid 13 through 37 Processing helix chain 'K' and resid 43 through 51 Processing helix chain 'N' and resid 14 through 45 Processing helix chain 'O' and resid 4 through 9 Processing helix chain 'O' and resid 13 through 37 Processing helix chain 'O' and resid 43 through 50 Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'Q' and resid 4 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 14 through 45 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 51 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'U' and resid 13 through 37 Processing helix chain 'U' and resid 43 through 50 Processing helix chain 'V' and resid 14 through 45 Processing helix chain 'W' and resid 13 through 37 Processing helix chain 'W' and resid 43 through 50 Processing helix chain 'X' and resid 14 through 45 Processing helix chain 'Y' and resid 13 through 37 Processing helix chain 'Y' and resid 43 through 50 Processing helix chain 'Z' and resid 14 through 45 Processing helix chain '1' and resid 13 through 37 Processing helix chain '1' and resid 43 through 50 Processing helix chain '2' and resid 14 through 45 Processing helix chain '7' and resid 4 through 9 Processing helix chain '7' and resid 13 through 37 Processing helix chain '8' and resid 14 through 45 Processing helix chain '9' and resid 4 through 9 Processing helix chain '9' and resid 13 through 37 Processing helix chain '9' and resid 43 through 50 Processing helix chain '0' and resid 14 through 45 Processing helix chain 'C' and resid 15 through 54 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'l' and resid 7 through 9 No H-bonds generated for 'chain 'l' and resid 7 through 9' Processing helix chain 'l' and resid 32 through 56 Processing helix chain 'l' and resid 71 through 73 No H-bonds generated for 'chain 'l' and resid 71 through 73' Processing helix chain 'l' and resid 80 through 82 No H-bonds generated for 'chain 'l' and resid 80 through 82' Processing helix chain 'l' and resid 84 through 111 Processing helix chain 'l' and resid 116 through 132 removed outlier: 3.521A pdb=" N PHE l 123 " --> pdb=" O PHE l 119 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Processing helix chain 'l' and resid 134 through 139 Processing helix chain 'l' and resid 142 through 144 No H-bonds generated for 'chain 'l' and resid 142 through 144' Processing helix chain 'l' and resid 152 through 164 removed outlier: 4.043A 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 219 Processing helix chain 'l' and resid 226 through 249 Processing helix chain 'l' and resid 259 through 267 removed outlier: 4.400A pdb=" N TRP l 265 " --> pdb=" O ASP l 261 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRP l 266 " --> pdb=" O TRP l 262 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL l 267 " --> pdb=" O TRP l 263 " (cutoff:3.500A) Processing helix chain 'm' and resid 37 through 41 removed outlier: 3.579A pdb=" N TRP m 41 " --> pdb=" O THR m 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 37 through 41' Processing helix chain 'm' and resid 54 through 78 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 Processing helix chain 'm' and resid 163 through 168 Processing helix chain 'm' and resid 171 through 173 No H-bonds generated for 'chain 'm' and resid 171 through 173' Processing helix chain 'm' and resid 179 through 192 Processing helix chain 'm' and resid 196 through 198 No H-bonds generated for 'chain 'm' and resid 196 through 198' Processing helix chain 'm' and resid 200 through 229 removed outlier: 4.919A pdb=" N ARG m 228 " --> pdb=" O LEU m 224 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N PHE m 229 " --> pdb=" O ALA m 225 " (cutoff:3.500A) Processing helix chain 'm' and resid 234 through 239 Processing helix chain 'm' and resid 243 through 256 Processing helix chain 'm' and resid 264 through 286 removed outlier: 3.984A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) Processing helix chain 'm' and resid 294 through 300 Processing helix chain 'h' and resid 12 through 36 Processing helix chain 'h' and resid 104 through 107 No H-bonds generated for 'chain 'h' and resid 104 through 107' Processing helix chain 'h' and resid 110 through 112 No H-bonds generated for 'chain 'h' and resid 110 through 112' Processing helix chain 'h' and resid 193 through 195 No H-bonds generated for 'chain 'h' and resid 193 through 195' Processing helix chain 'h' and resid 210 through 213 No H-bonds generated for 'chain 'h' and resid 210 through 213' Processing helix chain 'h' and resid 227 through 243 removed outlier: 4.196A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 251 through 259 Processing helix chain 'a' and resid 4 through 9 Processing helix chain 'a' and resid 13 through 37 Processing helix chain 'a' and resid 43 through 50 Processing helix chain 'b' and resid 14 through 45 Processing helix chain 'd' and resid 4 through 9 Processing helix chain 'd' and resid 13 through 37 Processing helix chain 'd' and resid 43 through 50 Processing helix chain 'e' and resid 14 through 45 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 14 through 45 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 50 Processing helix chain 'j' and resid 14 through 45 Processing helix chain 'k' and resid 4 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 14 through 45 Processing helix chain 'o' and resid 4 through 9 Processing helix chain 'o' and resid 13 through 37 Processing helix chain 'o' and resid 43 through 50 Processing helix chain 'p' and resid 14 through 45 Processing helix chain 'q' and resid 4 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 14 through 45 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 51 Processing helix chain 't' and resid 14 through 45 removed outlier: 3.662A pdb=" N VAL t 23 " --> pdb=" O GLU t 19 " (cutoff:3.500A) Processing helix chain 'u' and resid 13 through 37 Processing helix chain 'u' and resid 43 through 50 Processing helix chain 'v' and resid 14 through 45 Processing helix chain 'w' and resid 13 through 37 Processing helix chain 'w' and resid 43 through 50 Processing helix chain 'x' and resid 14 through 45 Processing helix chain 'y' and resid 13 through 37 Processing helix chain 'y' and resid 43 through 50 Processing helix chain 'z' and resid 14 through 45 Processing helix chain '5' and resid 13 through 37 Processing helix chain '5' and resid 43 through 50 Processing helix chain '4' and resid 14 through 45 Processing helix chain '6' and resid 4 through 9 Processing helix chain '6' and resid 13 through 37 Processing helix chain '6' and resid 43 through 45 No H-bonds generated for 'chain '6' and resid 43 through 45' Processing helix chain 'aa' and resid 14 through 45 Processing helix chain '3' and resid 4 through 9 Processing helix chain '3' and resid 13 through 37 Processing helix chain '3' and resid 43 through 50 Processing helix chain 'ab' and resid 14 through 45 Processing helix chain 'c' and resid 15 through 54 Processing helix chain 'c' and resid 56 through 58 No H-bonds generated for 'chain 'c' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'H' and resid 62 through 66 removed outlier: 4.493A pdb=" N GLY H 71 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.780A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 152 through 154 removed outlier: 3.786A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'h' and resid 62 through 66 removed outlier: 4.494A pdb=" N GLY h 71 " --> pdb=" O LEU h 66 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'h' and resid 87 through 89 Processing sheet with id= G, first strand: chain 'h' and resid 131 through 133 removed outlier: 6.780A pdb=" N GLU h 180 " --> pdb=" O VAL h 165 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE h 167 " --> pdb=" O PHE h 178 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE h 178 " --> pdb=" O ILE h 167 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'h' and resid 152 through 154 removed outlier: 3.784A pdb=" N GLY h 162 " --> pdb=" O VAL h 153 " (cutoff:3.500A) 2210 hydrogen bonds defined for protein. 6438 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: 12.97 Time building geometry restraints manager: 18.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.34: 11179 1.34 - 1.55: 31824 1.55 - 1.76: 269 1.76 - 1.97: 311 1.97 - 2.17: 256 Bond restraints: 43839 Sorted by residual: bond pdb=" C3C BPB l 306 " pdb=" CAC BPB l 306 " ideal model delta sigma weight residual 1.334 1.551 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C3C BPB L 305 " pdb=" CAC BPB L 305 " ideal model delta sigma weight residual 1.334 1.550 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C32 SPO s 105 " pdb=" C33 SPO s 105 " ideal model delta sigma weight residual 1.336 1.544 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C37 SPO s 104 " pdb=" C38 SPO s 104 " ideal model delta sigma weight residual 1.336 1.542 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C37 SPO 8 101 " pdb=" C38 SPO 8 101 " ideal model delta sigma weight residual 1.336 1.541 -0.205 2.00e-02 2.50e+03 1.05e+02 ... (remaining 43834 not shown) Histogram of bond angle deviations from ideal: 84.94 - 100.56: 294 100.56 - 116.19: 29352 116.19 - 131.82: 30065 131.82 - 147.44: 500 147.44 - 163.07: 128 Bond angle restraints: 60339 Sorted by residual: angle pdb=" C12 SPO e 103 " pdb=" C14 SPO e 103 " pdb=" C15 SPO e 103 " ideal model delta sigma weight residual 127.13 103.17 23.96 3.00e+00 1.11e-01 6.38e+01 angle pdb=" C10 SPO i 102 " pdb=" C9 SPO i 102 " pdb=" C7 SPO i 102 " ideal model delta sigma weight residual 127.14 103.22 23.92 3.00e+00 1.11e-01 6.36e+01 angle pdb=" C10 SPO e 103 " pdb=" C9 SPO e 103 " pdb=" C7 SPO e 103 " ideal model delta sigma weight residual 127.14 104.51 22.63 3.00e+00 1.11e-01 5.69e+01 angle pdb=" CB ARG h 177 " pdb=" CG ARG h 177 " pdb=" CD ARG h 177 " ideal model delta sigma weight residual 111.30 94.67 16.63 2.30e+00 1.89e-01 5.23e+01 angle pdb=" CB ARG H 177 " pdb=" CG ARG H 177 " pdb=" CD ARG H 177 " ideal model delta sigma weight residual 111.30 94.79 16.51 2.30e+00 1.89e-01 5.16e+01 ... (remaining 60334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 22184 35.93 - 71.86: 869 71.86 - 107.79: 66 107.79 - 143.72: 20 143.72 - 179.65: 5 Dihedral angle restraints: 23144 sinusoidal: 10524 harmonic: 12620 Sorted by residual: dihedral pdb=" C1 BCL m1301 " pdb=" C2 BCL m1301 " pdb=" C3 BCL m1301 " pdb=" C5 BCL m1301 " ideal model delta sinusoidal sigma weight residual -180.00 -0.35 -179.65 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL M1301 " pdb=" C2 BCL M1301 " pdb=" C3 BCL M1301 " pdb=" C5 BCL M1301 " ideal model delta sinusoidal sigma weight residual -180.00 -0.46 -179.54 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" CA GLU l 201 " pdb=" C GLU l 201 " pdb=" N LYS l 202 " pdb=" CA LYS l 202 " ideal model delta harmonic sigma weight residual 180.00 -131.67 -48.33 0 5.00e+00 4.00e-02 9.34e+01 ... (remaining 23141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 5521 0.090 - 0.181: 377 0.181 - 0.271: 17 0.271 - 0.361: 4 0.361 - 0.452: 1 Chirality restraints: 5920 Sorted by residual: chirality pdb=" CB THR o 38 " pdb=" CA THR o 38 " pdb=" OG1 THR o 38 " pdb=" CG2 THR o 38 " both_signs ideal model delta sigma weight residual False 2.55 2.10 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CG LEU h 241 " pdb=" CB LEU h 241 " pdb=" CD1 LEU h 241 " pdb=" CD2 LEU h 241 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CG LEU H 241 " pdb=" CB LEU H 241 " pdb=" CD1 LEU H 241 " pdb=" CD2 LEU H 241 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 5917 not shown) Planarity restraints: 7401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C31 SPO 9 102 " 0.541 2.00e-02 2.50e+03 4.85e-01 2.95e+03 pdb=" C32 SPO 9 102 " -0.669 2.00e-02 2.50e+03 pdb=" C33 SPO 9 102 " -0.468 2.00e-02 2.50e+03 pdb=" C34 SPO 9 102 " 0.444 2.00e-02 2.50e+03 pdb=" C35 SPO 9 102 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C31 SPO 3 101 " -0.541 2.00e-02 2.50e+03 4.85e-01 2.94e+03 pdb=" C32 SPO 3 101 " 0.665 2.00e-02 2.50e+03 pdb=" C33 SPO 3 101 " 0.471 2.00e-02 2.50e+03 pdb=" C34 SPO 3 101 " -0.447 2.00e-02 2.50e+03 pdb=" C35 SPO 3 101 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C31 SPO D 102 " 0.538 2.00e-02 2.50e+03 4.84e-01 2.93e+03 pdb=" C32 SPO D 102 " -0.662 2.00e-02 2.50e+03 pdb=" C33 SPO D 102 " -0.473 2.00e-02 2.50e+03 pdb=" C34 SPO D 102 " 0.448 2.00e-02 2.50e+03 pdb=" C35 SPO D 102 " 0.148 2.00e-02 2.50e+03 ... (remaining 7398 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 325 2.57 - 3.16: 32388 3.16 - 3.74: 66784 3.74 - 4.32: 98316 4.32 - 4.90: 158635 Nonbonded interactions: 356448 Sorted by model distance: nonbonded pdb=" OG1 THR K 38 " pdb=" O SER K 40 " model vdw 1.992 2.440 nonbonded pdb=" OH TYR y 41 " pdb=" OG SER 5 47 " model vdw 2.018 2.440 nonbonded pdb=" O LYS 7 3 " pdb=" NZ LYS 7 6 " model vdw 2.028 2.520 nonbonded pdb=" OE1 GLN f 20 " pdb=" OH TYR g 24 " model vdw 2.058 2.440 nonbonded pdb=" OE1 GLN s 20 " pdb=" OH TYR t 24 " model vdw 2.078 2.440 ... (remaining 356443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '0' and resid 12 through 49) selection = (chain '8' and resid 12 through 49) selection = (chain 'B' and resid 12 through 49) selection = (chain 'E' and resid 12 through 49) selection = (chain 'G' and resid 12 through 49) selection = (chain 'J' and resid 12 through 49) selection = (chain 'N' and resid 12 through 49) selection = (chain 'R' and resid 12 through 49) selection = (chain 'T' and resid 12 through 49) selection = (chain 'aa' and resid 12 through 49) selection = (chain 'ab' and resid 12 through 49) selection = (chain 'b' and resid 12 through 49) selection = (chain 'e' and resid 12 through 49) selection = (chain 'g' and resid 12 through 49) selection = (chain 'j' and resid 12 through 49) } ncs_group { reference = chain '1' selection = (chain '5' and (resid 12 through 54 or resid 101)) selection = (chain 'U' and (resid 12 through 54 or (resid 101 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )))) selection = chain 'W' selection = chain 'Y' selection = (chain 'u' and (resid 12 through 54 or (resid 101 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )))) selection = chain 'w' selection = chain 'y' } ncs_group { reference = (chain '2' and resid 13 through 48) selection = chain '4' selection = (chain 'P' and resid 13 through 48) selection = (chain 'V' and resid 13 through 48) selection = (chain 'X' and resid 13 through 48) selection = (chain 'Z' and resid 13 through 48) selection = (chain 'n' and resid 13 through 48) selection = (chain 'p' and resid 13 through 48) selection = (chain 'r' and resid 13 through 48) selection = (chain 't' and resid 13 through 48) selection = (chain 'v' and resid 13 through 48) selection = (chain 'x' and resid 13 through 48) selection = (chain 'z' and resid 13 through 48) } ncs_group { reference = (chain '3' and resid 1 through 54) selection = (chain '9' and resid 1 through 54) selection = (chain 'A' and resid 1 through 54) selection = (chain 'D' and resid 1 through 54) selection = (chain 'F' and resid 1 through 54) selection = (chain 'I' and resid 1 through 54) selection = (chain 'K' and resid 1 through 54) selection = (chain 'O' and resid 1 through 54) selection = (chain 'Q' and resid 1 through 54) selection = (chain 'S' and resid 1 through 54) selection = (chain 'a' and resid 1 through 54) selection = (chain 'd' and resid 1 through 54) selection = (chain 'f' and resid 1 through 54) selection = (chain 'i' and resid 1 through 54) selection = (chain 'k' and resid 1 through 54) selection = (chain 'o' and resid 1 through 54) selection = (chain 'q' and resid 1 through 54) selection = (chain 's' and resid 1 through 54) } ncs_group { reference = chain '6' selection = (chain '7' and resid 1 through 46) } ncs_group { reference = (chain 'C' and resid 5 through 69) selection = (chain 'c' and resid 5 through 69) } ncs_group { reference = chain 'H' selection = (chain 'h' and resid 1 through 260) } ncs_group { reference = (chain 'L' and (resid 1 through 281 or resid 301 through 303)) selection = (chain 'l' and (resid 1 through 281 or resid 301 through 302 or (resid 303 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C18 or name C19 or name C1M or name C2 or name C \ 20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or na \ me C27 or name C28 or name C29 or name C3 or name C30 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C3M or name C4 or name C4M \ or name C5 or name C6 or name C7 or name C8 or name C9 or name O2 or name O3 or \ name O4 or name O5 )))) } ncs_group { reference = (chain 'M' and (resid 2 through 306 or resid 1301 through 1306)) selection = chain 'm' } 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 15 5.49 5 Mg 64 5.21 5 S 162 5.16 5 C 29574 2.51 5 N 5997 2.21 5 O 6362 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: 12.710 Check model and map are aligned: 0.670 Convert atoms to be neutral: 0.390 Process input model: 98.280 Find NCS groups from input model: 3.230 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 0.217 43839 Z= 1.022 Angle : 2.121 23.957 60339 Z= 0.780 Chirality : 0.049 0.452 5920 Planarity : 0.051 0.485 7401 Dihedral : 18.344 179.655 15008 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.13), residues: 4222 helix: 1.99 (0.09), residues: 2880 sheet: -1.66 (0.67), residues: 46 loop : -1.64 (0.15), residues: 1296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 698 time to evaluate : 5.422 Fit side-chains outliers start: 103 outliers final: 6 residues processed: 744 average time/residue: 0.5458 time to fit residues: 674.8488 Evaluate side-chains 530 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 524 time to evaluate : 4.290 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4001 time to fit residues: 10.3321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 342 optimal weight: 0.6980 chunk 307 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 207 optimal weight: 0.7980 chunk 164 optimal weight: 8.9990 chunk 318 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 193 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 368 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 GLN 2 21 HIS ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 199 GLN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 21 HIS ** y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** aa 16 GLN 3 20 GLN ab 18 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 43839 Z= 0.249 Angle : 0.860 15.511 60339 Z= 0.336 Chirality : 0.040 0.155 5920 Planarity : 0.006 0.060 7401 Dihedral : 16.754 179.947 7330 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.12), residues: 4222 helix: 2.67 (0.09), residues: 2770 sheet: -1.25 (0.71), residues: 46 loop : -0.91 (0.15), residues: 1406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 593 time to evaluate : 4.315 Fit side-chains outliers start: 43 outliers final: 27 residues processed: 618 average time/residue: 0.5056 time to fit residues: 525.8331 Evaluate side-chains 574 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 547 time to evaluate : 4.027 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3795 time to fit residues: 24.5377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 204 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 306 optimal weight: 6.9990 chunk 251 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 369 optimal weight: 4.9990 chunk 399 optimal weight: 5.9990 chunk 328 optimal weight: 0.9980 chunk 366 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 296 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 21 HIS X 16 GLN b 16 GLN ** b 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ab 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 43839 Z= 0.181 Angle : 0.714 14.562 60339 Z= 0.277 Chirality : 0.036 0.140 5920 Planarity : 0.005 0.063 7401 Dihedral : 15.767 179.537 7330 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.12), residues: 4222 helix: 2.98 (0.09), residues: 2782 sheet: -0.74 (0.74), residues: 46 loop : -0.74 (0.16), residues: 1394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 583 time to evaluate : 4.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 600 average time/residue: 0.5094 time to fit residues: 513.1522 Evaluate side-chains 562 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 552 time to evaluate : 4.076 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3711 time to fit residues: 12.2141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 364 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 370 optimal weight: 10.0000 chunk 392 optimal weight: 5.9990 chunk 193 optimal weight: 0.4980 chunk 351 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 35 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ab 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 43839 Z= 0.215 Angle : 0.737 14.145 60339 Z= 0.288 Chirality : 0.038 0.143 5920 Planarity : 0.005 0.063 7401 Dihedral : 15.492 179.490 7330 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.13), residues: 4222 helix: 2.60 (0.09), residues: 2888 sheet: -0.61 (0.75), residues: 46 loop : -0.84 (0.17), residues: 1288 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 578 time to evaluate : 4.127 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 26 residues processed: 605 average time/residue: 0.5449 time to fit residues: 558.5090 Evaluate side-chains 576 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 550 time to evaluate : 4.134 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4724 time to fit residues: 26.8394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 326 optimal weight: 0.7980 chunk 222 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 292 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 334 optimal weight: 0.8980 chunk 271 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 352 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 HIS ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 43839 Z= 0.165 Angle : 0.675 13.837 60339 Z= 0.261 Chirality : 0.036 0.138 5920 Planarity : 0.004 0.064 7401 Dihedral : 15.018 179.339 7330 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.13), residues: 4222 helix: 2.80 (0.09), residues: 2880 sheet: -0.46 (0.77), residues: 46 loop : -0.68 (0.17), residues: 1296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 582 time to evaluate : 4.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 596 average time/residue: 0.5027 time to fit residues: 506.0612 Evaluate side-chains 561 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 551 time to evaluate : 4.138 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3703 time to fit residues: 12.2151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 132 optimal weight: 1.9990 chunk 353 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 392 optimal weight: 0.9990 chunk 326 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 ASN h 35 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 43839 Z= 0.171 Angle : 0.681 13.773 60339 Z= 0.262 Chirality : 0.036 0.220 5920 Planarity : 0.004 0.063 7401 Dihedral : 14.865 179.365 7330 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.13), residues: 4222 helix: 2.83 (0.09), residues: 2880 sheet: -0.44 (0.77), residues: 46 loop : -0.65 (0.17), residues: 1296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 564 time to evaluate : 4.022 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 576 average time/residue: 0.4979 time to fit residues: 483.9720 Evaluate side-chains 558 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 543 time to evaluate : 4.038 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3742 time to fit residues: 15.7833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 378 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 223 optimal weight: 0.0570 chunk 286 optimal weight: 2.9990 chunk 222 optimal weight: 0.5980 chunk 330 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 391 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 GLN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 43839 Z= 0.143 Angle : 0.646 13.716 60339 Z= 0.248 Chirality : 0.035 0.213 5920 Planarity : 0.004 0.063 7401 Dihedral : 14.517 179.311 7330 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.13), residues: 4222 helix: 2.96 (0.09), residues: 2882 sheet: -0.27 (0.80), residues: 46 loop : -0.58 (0.17), residues: 1294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 564 time to evaluate : 4.223 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 2 residues processed: 571 average time/residue: 0.5013 time to fit residues: 488.1867 Evaluate side-chains 540 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 538 time to evaluate : 4.137 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3595 time to fit residues: 6.8174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 242 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 233 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 248 optimal weight: 5.9990 chunk 266 optimal weight: 0.0770 chunk 193 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 307 optimal weight: 0.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 300 ASN h 35 ASN a 20 GLN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 43839 Z= 0.142 Angle : 0.642 13.683 60339 Z= 0.246 Chirality : 0.035 0.183 5920 Planarity : 0.004 0.063 7401 Dihedral : 14.318 179.351 7330 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.13), residues: 4222 helix: 3.00 (0.09), residues: 2882 sheet: -0.12 (0.82), residues: 46 loop : -0.52 (0.17), residues: 1294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 549 time to evaluate : 4.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 559 average time/residue: 0.5122 time to fit residues: 485.3301 Evaluate side-chains 538 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 532 time to evaluate : 4.126 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4720 time to fit residues: 10.1504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 355 optimal weight: 6.9990 chunk 374 optimal weight: 7.9990 chunk 342 optimal weight: 6.9990 chunk 364 optimal weight: 10.0000 chunk 219 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 286 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 329 optimal weight: 7.9990 chunk 344 optimal weight: 9.9990 chunk 363 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 5 ASN A 20 GLN E 18 GLN ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 21 HIS C 60 ASN h 206 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 52 ASN 5 20 GLN ** c 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.096 43839 Z= 0.475 Angle : 0.940 15.699 60339 Z= 0.374 Chirality : 0.047 0.189 5920 Planarity : 0.006 0.067 7401 Dihedral : 16.045 179.434 7330 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.12), residues: 4222 helix: 2.02 (0.09), residues: 2894 sheet: -0.78 (0.72), residues: 48 loop : -0.88 (0.17), residues: 1280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 526 time to evaluate : 3.929 Fit side-chains outliers start: 32 outliers final: 19 residues processed: 544 average time/residue: 0.5400 time to fit residues: 496.3519 Evaluate side-chains 530 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 511 time to evaluate : 4.135 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4039 time to fit residues: 19.5693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 239 optimal weight: 0.0980 chunk 385 optimal weight: 0.7980 chunk 235 optimal weight: 0.5980 chunk 182 optimal weight: 0.8980 chunk 268 optimal weight: 1.9990 chunk 404 optimal weight: 2.9990 chunk 372 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 197 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 GLN 7 20 GLN h 206 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 20 GLN 6 20 GLN c 66 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 43839 Z= 0.153 Angle : 0.675 14.541 60339 Z= 0.263 Chirality : 0.036 0.170 5920 Planarity : 0.004 0.066 7401 Dihedral : 14.844 179.365 7330 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.13), residues: 4222 helix: 2.69 (0.09), residues: 2882 sheet: -0.30 (0.78), residues: 48 loop : -0.57 (0.17), residues: 1292 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 546 time to evaluate : 3.932 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 548 average time/residue: 0.5119 time to fit residues: 474.7700 Evaluate side-chains 537 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 533 time to evaluate : 4.142 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3823 time to fit residues: 8.0458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 255 optimal weight: 3.9990 chunk 343 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 296 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 322 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 331 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 35 ASN h 206 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.168379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.134915 restraints weight = 45899.446| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.80 r_work: 0.3066 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 43839 Z= 0.170 Angle : 0.679 15.213 60339 Z= 0.263 Chirality : 0.036 0.175 5920 Planarity : 0.004 0.064 7401 Dihedral : 14.647 179.545 7330 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.13), residues: 4222 helix: 2.78 (0.09), residues: 2880 sheet: -0.22 (0.78), residues: 48 loop : -0.52 (0.17), residues: 1294 =============================================================================== Job complete usr+sys time: 9380.69 seconds wall clock time: 170 minutes 1.16 seconds (10201.16 seconds total)