Starting phenix.real_space_refine on Sun Mar 24 14:47:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7va9_31835/03_2024/7va9_31835_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7va9_31835/03_2024/7va9_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_31835/03_2024/7va9_31835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7va9_31835/03_2024/7va9_31835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7va9_31835/03_2024/7va9_31835_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7va9_31835/03_2024/7va9_31835_updated.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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-5265/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: 40 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: 19 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: 19.65, per 1000 atoms: 0.47 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: 17.29 Conformation dependent library (CDL) restraints added in 6.9 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: 6.16 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: 12.36 Time building geometry restraints manager: 18.70 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: 22402 35.93 - 71.86: 913 71.86 - 107.79: 87 107.79 - 143.72: 20 143.72 - 179.65: 9 Dihedral angle restraints: 23431 sinusoidal: 10811 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 23428 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 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 10.080 Check model and map are aligned: 0.510 Set scattering table: 0.320 Process input model: 100.380 Find NCS groups from input model: 3.260 Set up NCS constraints: 0.580 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 18.940 179.655 15295 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.83 % Allowed : 2.36 % Favored : 94.80 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP L 272 HIS 0.011 0.002 HIS p 39 PHE 0.080 0.003 PHE m 216 TYR 0.066 0.003 TYR H 236 ARG 0.021 0.002 ARG D 15 *********************** 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 : 4.379 Fit side-chains REVERT: H 232 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7565 (mtpp) REVERT: J 40 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8212 (mm) REVERT: W 26 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6254 (tp) REVERT: C 61 GLN cc_start: 0.7258 (tp40) cc_final: 0.6793 (tp40) REVERT: l 47 ILE cc_start: 0.8230 (mm) cc_final: 0.8002 (mm) REVERT: m 2 GLU cc_start: 0.4637 (tt0) cc_final: 0.4082 (tt0) REVERT: m 4 GLN cc_start: 0.8659 (mm110) cc_final: 0.8259 (mm110) REVERT: h 81 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.5119 (mt-10) REVERT: k 1 MET cc_start: 0.5215 (tmm) cc_final: 0.4765 (tmm) REVERT: 6 2 SER cc_start: 0.7303 (p) cc_final: 0.6946 (m) outliers start: 103 outliers final: 6 residues processed: 744 average time/residue: 0.5059 time to fit residues: 621.4046 Evaluate side-chains 534 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 524 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain M residue 287 SER Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain h residue 4 VAL Chi-restraints excluded: chain h residue 81 GLU Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain 5 residue 30 MET 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: 3.9990 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: 0.7794 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 43839 Z= 0.247 Angle : 0.861 15.577 60339 Z= 0.336 Chirality : 0.040 0.229 5920 Planarity : 0.005 0.060 7401 Dihedral : 17.572 179.973 7637 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.29 % Allowed : 6.29 % Favored : 92.41 % 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: 2.23 (0.12), residues: 4222 helix: 2.65 (0.09), residues: 2770 sheet: -1.25 (0.71), residues: 46 loop : -0.91 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 272 HIS 0.013 0.002 HIS m 182 PHE 0.046 0.002 PHE m 216 TYR 0.048 0.002 TYRaa 24 ARG 0.009 0.001 ARG G 46 *********************** 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 641 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 594 time to evaluate : 4.135 Fit side-chains REVERT: H 103 ASP cc_start: 0.7639 (t70) cc_final: 0.7431 (t70) REVERT: A 45 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6409 (mm-30) REVERT: F 3 LYS cc_start: 0.7784 (mtpp) cc_final: 0.7577 (mttm) REVERT: I 3 LYS cc_start: 0.6512 (mttp) cc_final: 0.6017 (mttm) REVERT: I 45 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6449 (mt-10) REVERT: W 26 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6736 (tp) REVERT: Y 30 MET cc_start: 0.3563 (mtp) cc_final: 0.3033 (mmt) REVERT: m 26 LEU cc_start: 0.8159 (mp) cc_final: 0.7916 (mp) REVERT: h 220 LYS cc_start: 0.7154 (ttpp) cc_final: 0.6707 (tmmt) REVERT: h 228 LEU cc_start: 0.8034 (tp) cc_final: 0.7794 (tp) REVERT: b 40 LEU cc_start: 0.8160 (mt) cc_final: 0.7958 (tp) REVERT: i 1 MET cc_start: 0.3406 (tmm) cc_final: 0.2993 (tpp) REVERT: q 9 MET cc_start: 0.6354 (mtm) cc_final: 0.6105 (mpp) REVERT: y 30 MET cc_start: 0.3483 (ttt) cc_final: 0.3132 (ttp) REVERT: z 25 MET cc_start: 0.2602 (mtm) cc_final: 0.2007 (tmm) outliers start: 47 outliers final: 28 residues processed: 622 average time/residue: 0.5011 time to fit residues: 522.7999 Evaluate side-chains 578 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 548 time to evaluate : 4.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain m residue 279 THR Chi-restraints excluded: chain h residue 4 VAL Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 211 ASP Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 47 SER Chi-restraints excluded: chain p residue 30 LEU Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain ab residue 26 SER Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 204 optimal weight: 0.0370 chunk 114 optimal weight: 0.7980 chunk 306 optimal weight: 7.9990 chunk 251 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 369 optimal weight: 4.9990 chunk 399 optimal weight: 5.9990 chunk 328 optimal weight: 0.9990 chunk 366 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 296 optimal weight: 0.9980 overall best weight: 0.7662 ------------------------------------------------------------------------------- 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 ** y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ab 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43839 Z= 0.153 Angle : 0.689 14.358 60339 Z= 0.266 Chirality : 0.036 0.206 5920 Planarity : 0.004 0.062 7401 Dihedral : 16.244 179.441 7620 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.99 % Allowed : 7.53 % Favored : 91.48 % 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: 2.81 (0.12), residues: 4222 helix: 3.09 (0.09), residues: 2772 sheet: -0.65 (0.76), residues: 46 loop : -0.70 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP l 272 HIS 0.010 0.001 HIS v 21 PHE 0.031 0.001 PHE k 23 TYR 0.019 0.001 TYR G 24 ARG 0.005 0.000 ARGab 46 *********************** 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 634 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 598 time to evaluate : 4.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7444 (pm20) REVERT: M 86 LEU cc_start: 0.7563 (tt) cc_final: 0.7248 (mt) REVERT: F 3 LYS cc_start: 0.7787 (mtpp) cc_final: 0.7402 (mptt) REVERT: I 1 MET cc_start: 0.1846 (tpt) cc_final: 0.1075 (tmm) REVERT: N 29 TRP cc_start: 0.6658 (m100) cc_final: 0.6287 (m100) REVERT: W 26 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6750 (tp) REVERT: C 27 MET cc_start: 0.8310 (mtt) cc_final: 0.7894 (mtt) REVERT: h 191 LEU cc_start: 0.8241 (mt) cc_final: 0.7896 (tp) REVERT: h 220 LYS cc_start: 0.7055 (ttpp) cc_final: 0.6589 (tptt) REVERT: h 231 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7691 (m-30) REVERT: a 1 MET cc_start: 0.5940 (tpt) cc_final: 0.5444 (tpt) REVERT: b 40 LEU cc_start: 0.8200 (mt) cc_final: 0.7948 (tp) REVERT: d 30 MET cc_start: 0.7974 (ttt) cc_final: 0.7759 (ttm) REVERT: k 1 MET cc_start: 0.6058 (tmm) cc_final: 0.5803 (tmm) REVERT: q 9 MET cc_start: 0.6411 (mtm) cc_final: 0.6201 (mpp) REVERT: s 9 MET cc_start: 0.5262 (mmp) cc_final: 0.5043 (mmp) REVERT: u 23 PHE cc_start: 0.7863 (t80) cc_final: 0.7309 (t80) REVERT: y 30 MET cc_start: 0.3502 (ttt) cc_final: 0.3184 (ttp) REVERT: z 25 MET cc_start: 0.2667 (mtm) cc_final: 0.1829 (tmm) outliers start: 36 outliers final: 13 residues processed: 616 average time/residue: 0.4965 time to fit residues: 511.2528 Evaluate side-chains 567 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 551 time to evaluate : 4.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain l residue 216 PHE Chi-restraints excluded: chain m residue 195 ASN Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 211 ASP Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain o residue 47 SER Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain c residue 67 ILE 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: 6.9990 chunk 191 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 370 optimal weight: 9.9990 chunk 392 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 351 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 5 ASN H 35 ASN ** W 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 43839 Z= 0.425 Angle : 0.939 16.432 60339 Z= 0.373 Chirality : 0.045 0.166 5920 Planarity : 0.006 0.086 7401 Dihedral : 17.198 179.819 7619 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.25 % Allowed : 8.91 % Favored : 88.84 % 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: 1.85 (0.12), residues: 4222 helix: 2.22 (0.09), residues: 2784 sheet: -1.00 (0.70), residues: 46 loop : -0.80 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP l 272 HIS 0.014 0.002 HIS l 153 PHE 0.029 0.003 PHE H 140 TYR 0.048 0.003 TYR F 41 ARG 0.007 0.001 ARGab 46 *********************** 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 639 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 557 time to evaluate : 4.094 Fit side-chains revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7598 (pm20) REVERT: H 81 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5536 (pt0) REVERT: B 19 GLU cc_start: 0.6884 (tt0) cc_final: 0.6679 (tt0) REVERT: F 3 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7456 (mptt) REVERT: N 29 TRP cc_start: 0.6757 (m100) cc_final: 0.6315 (m100) REVERT: Q 26 LEU cc_start: 0.8589 (mt) cc_final: 0.8317 (mt) REVERT: W 26 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6911 (tp) REVERT: 0 15 GLU cc_start: 0.6726 (pm20) cc_final: 0.6366 (pm20) REVERT: C 6 ILE cc_start: 0.4332 (OUTLIER) cc_final: 0.3938 (tp) REVERT: C 61 GLN cc_start: 0.7882 (tp40) cc_final: 0.7589 (tp40) REVERT: m 86 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7658 (tp) REVERT: h 160 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7684 (mp) REVERT: h 197 LYS cc_start: 0.8076 (tptp) cc_final: 0.7544 (tttt) REVERT: h 220 LYS cc_start: 0.7104 (ttpp) cc_final: 0.6749 (tmmt) REVERT: b 46 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7752 (ttt180) REVERT: k 1 MET cc_start: 0.6344 (tmm) cc_final: 0.5800 (tmm) REVERT: k 45 GLU cc_start: 0.6216 (mm-30) cc_final: 0.5812 (mm-30) REVERT: q 9 MET cc_start: 0.6299 (mtm) cc_final: 0.6035 (mpp) REVERT: v 25 MET cc_start: 0.5907 (mmm) cc_final: 0.5595 (mmt) REVERT: z 25 MET cc_start: 0.2513 (mtm) cc_final: 0.1875 (tmm) REVERT: 3 3 LYS cc_start: 0.7448 (pttp) cc_final: 0.7216 (mtmm) REVERT: c 33 TRP cc_start: 0.8474 (m100) cc_final: 0.8263 (m100) outliers start: 82 outliers final: 46 residues processed: 611 average time/residue: 0.5140 time to fit residues: 523.1974 Evaluate side-chains 580 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 527 time to evaluate : 4.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 289 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 9 residue 54 VAL Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain m residue 279 THR Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 46 ASP Chi-restraints excluded: chain h residue 160 ILE Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain h residue 211 ASP Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 247 LYS Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain b residue 46 ARG Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 44 ILE Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain u residue 47 SER Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 60 ASN Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 326 optimal weight: 0.8980 chunk 222 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 292 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 334 optimal weight: 0.6980 chunk 271 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 352 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 5 ASN H 35 ASN 7 20 GLN h 35 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 GLN c 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 43839 Z= 0.207 Angle : 0.726 14.007 60339 Z= 0.284 Chirality : 0.037 0.199 5920 Planarity : 0.005 0.064 7401 Dihedral : 16.233 179.487 7619 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.84 % Allowed : 10.20 % Favored : 87.96 % 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: 2.18 (0.13), residues: 4222 helix: 2.42 (0.09), residues: 2880 sheet: -0.69 (0.75), residues: 46 loop : -0.77 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP l 271 HIS 0.011 0.001 HIS M 182 PHE 0.026 0.001 PHE k 23 TYR 0.019 0.001 TYR A 41 ARG 0.009 0.001 ARG J 46 *********************** 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 642 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 575 time to evaluate : 4.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7382 (pm20) REVERT: M 86 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7589 (mt) REVERT: H 81 GLU cc_start: 0.6025 (OUTLIER) cc_final: 0.4415 (mm-30) REVERT: F 3 LYS cc_start: 0.7860 (mtpp) cc_final: 0.7395 (mptt) REVERT: J 29 TRP cc_start: 0.7386 (m100) cc_final: 0.7017 (m100) REVERT: N 29 TRP cc_start: 0.6768 (m100) cc_final: 0.6246 (m100) REVERT: W 26 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6803 (tp) REVERT: 7 3 LYS cc_start: 0.7897 (tttt) cc_final: 0.7654 (tttp) REVERT: 0 15 GLU cc_start: 0.6568 (pm20) cc_final: 0.6256 (pm20) REVERT: h 197 LYS cc_start: 0.8091 (tptp) cc_final: 0.7580 (tttt) REVERT: h 220 LYS cc_start: 0.7055 (ttpp) cc_final: 0.6611 (tptt) REVERT: h 231 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: h 236 TYR cc_start: 0.8303 (t80) cc_final: 0.8024 (t80) REVERT: k 1 MET cc_start: 0.6353 (tmm) cc_final: 0.5819 (tmm) REVERT: k 42 ASN cc_start: 0.8089 (t0) cc_final: 0.7842 (t0) REVERT: k 45 GLU cc_start: 0.6141 (mm-30) cc_final: 0.5906 (mm-30) REVERT: q 9 MET cc_start: 0.6354 (mtm) cc_final: 0.6115 (mpp) REVERT: v 25 MET cc_start: 0.5996 (mmm) cc_final: 0.5629 (mmt) REVERT: z 25 MET cc_start: 0.2336 (mtm) cc_final: 0.1783 (tmm) REVERT: 3 45 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7309 (mt-10) REVERT: c 58 GLN cc_start: 0.7490 (tp40) cc_final: 0.7194 (tp-100) outliers start: 67 outliers final: 47 residues processed: 612 average time/residue: 0.5099 time to fit residues: 521.8266 Evaluate side-chains 607 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 555 time to evaluate : 4.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 9 residue 54 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 195 ASN Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain m residue 279 THR Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 202 ARG Chi-restraints excluded: chain h residue 211 ASP Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 228 LEU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain i residue 47 SER Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain u residue 47 SER Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 60 ASN Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 132 optimal weight: 8.9990 chunk 353 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 230 optimal weight: 0.0370 chunk 96 optimal weight: 3.9990 chunk 392 optimal weight: 3.9990 chunk 326 optimal weight: 0.6980 chunk 181 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 overall best weight: 1.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 5 ASN ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN h 35 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 43839 Z= 0.215 Angle : 0.730 13.876 60339 Z= 0.285 Chirality : 0.038 0.189 5920 Planarity : 0.005 0.064 7401 Dihedral : 15.943 179.585 7619 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.98 % Allowed : 11.11 % Favored : 86.92 % 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: 2.29 (0.13), residues: 4222 helix: 2.50 (0.09), residues: 2876 sheet: -0.74 (0.73), residues: 48 loop : -0.72 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Q 8 HIS 0.011 0.001 HIS l 153 PHE 0.028 0.002 PHE k 23 TYR 0.021 0.001 TYR F 41 ARG 0.008 0.001 ARG J 46 *********************** 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 637 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 565 time to evaluate : 4.437 Fit side-chains revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7471 (pm20) REVERT: M 86 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7611 (mt) REVERT: H 81 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.4389 (mm-30) REVERT: H 159 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6072 (tp30) REVERT: F 3 LYS cc_start: 0.7890 (mtpp) cc_final: 0.7357 (mptt) REVERT: N 29 TRP cc_start: 0.6812 (m100) cc_final: 0.6257 (m100) REVERT: W 26 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6758 (tp) REVERT: W 41 TYR cc_start: 0.6512 (m-80) cc_final: 0.6207 (m-80) REVERT: Y 30 MET cc_start: 0.3631 (OUTLIER) cc_final: 0.2942 (mmt) REVERT: 0 15 GLU cc_start: 0.6648 (pm20) cc_final: 0.6345 (pm20) REVERT: h 160 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7474 (mp) REVERT: h 191 LEU cc_start: 0.8568 (mt) cc_final: 0.8258 (mt) REVERT: h 197 LYS cc_start: 0.8102 (tptp) cc_final: 0.7634 (tttt) REVERT: h 231 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: b 46 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7751 (ttt180) REVERT: k 1 MET cc_start: 0.6423 (tmm) cc_final: 0.5886 (tmm) REVERT: q 9 MET cc_start: 0.6424 (mtm) cc_final: 0.6167 (mpp) REVERT: s 8 TRP cc_start: 0.5617 (m100) cc_final: 0.4941 (m100) REVERT: s 9 MET cc_start: 0.5888 (mtm) cc_final: 0.5477 (mtp) REVERT: v 25 MET cc_start: 0.6001 (mmm) cc_final: 0.5665 (mmt) REVERT: z 25 MET cc_start: 0.2249 (mtm) cc_final: 0.1760 (tmm) REVERT: c 58 GLN cc_start: 0.7435 (tp40) cc_final: 0.7130 (tp-100) outliers start: 72 outliers final: 48 residues processed: 605 average time/residue: 0.5060 time to fit residues: 510.5363 Evaluate side-chains 603 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 546 time to evaluate : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 9 residue 54 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 195 ASN Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain m residue 279 THR Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 160 ILE Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 211 ASP Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 247 LYS Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain b residue 46 ARG Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain i residue 47 SER Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain u residue 47 SER Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 60 ASN Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 378 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 286 optimal weight: 0.7980 chunk 222 optimal weight: 0.3980 chunk 330 optimal weight: 10.0000 chunk 219 optimal weight: 0.7980 chunk 391 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 5 ASN G 16 GLN C 66 ASN m 300 ASN h 35 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43839 Z= 0.157 Angle : 0.664 14.231 60339 Z= 0.258 Chirality : 0.036 0.174 5920 Planarity : 0.004 0.063 7401 Dihedral : 15.493 179.505 7619 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.84 % Allowed : 11.49 % Favored : 86.67 % 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: 2.62 (0.13), residues: 4222 helix: 2.75 (0.09), residues: 2878 sheet: -0.45 (0.76), residues: 48 loop : -0.61 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 157 HIS 0.008 0.001 HIS l 153 PHE 0.025 0.001 PHE k 23 TYR 0.014 0.001 TYR F 41 ARG 0.005 0.000 ARG J 46 *********************** 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 624 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 557 time to evaluate : 3.327 Fit side-chains revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7485 (pm20) REVERT: H 81 GLU cc_start: 0.5853 (OUTLIER) cc_final: 0.4283 (mm-30) REVERT: H 159 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6140 (tp30) REVERT: F 3 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7353 (mptt) REVERT: N 29 TRP cc_start: 0.6705 (m100) cc_final: 0.6095 (m100) REVERT: O 25 PHE cc_start: 0.8859 (t80) cc_final: 0.8608 (t80) REVERT: S 33 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8422 (mp) REVERT: W 26 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6676 (tp) REVERT: Y 30 MET cc_start: 0.3700 (OUTLIER) cc_final: 0.3034 (mmt) REVERT: 0 15 GLU cc_start: 0.6638 (pm20) cc_final: 0.6265 (pm20) REVERT: l 59 TRP cc_start: 0.8246 (m100) cc_final: 0.7951 (m100) REVERT: h 170 ASP cc_start: 0.6983 (t0) cc_final: 0.6601 (t0) REVERT: h 191 LEU cc_start: 0.8495 (mt) cc_final: 0.8209 (mt) REVERT: h 197 LYS cc_start: 0.8082 (tptp) cc_final: 0.7625 (tttt) REVERT: h 231 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7544 (m-30) REVERT: k 1 MET cc_start: 0.6358 (tmm) cc_final: 0.5791 (tmm) REVERT: q 9 MET cc_start: 0.6457 (mtm) cc_final: 0.6214 (mpp) REVERT: s 9 MET cc_start: 0.5770 (mtm) cc_final: 0.5267 (mtp) REVERT: u 52 ASN cc_start: 0.5986 (OUTLIER) cc_final: 0.5707 (t0) REVERT: v 25 MET cc_start: 0.5933 (mmm) cc_final: 0.5636 (mmt) REVERT: x 25 MET cc_start: 0.4653 (tpp) cc_final: 0.4105 (tpp) REVERT: z 25 MET cc_start: 0.1997 (mtm) cc_final: 0.1608 (tmm) REVERT: c 58 GLN cc_start: 0.7392 (tp40) cc_final: 0.7073 (tp-100) outliers start: 67 outliers final: 43 residues processed: 595 average time/residue: 0.5055 time to fit residues: 506.6149 Evaluate side-chains 592 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 541 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 9 residue 54 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain m residue 279 THR Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 202 ARG Chi-restraints excluded: chain h residue 211 ASP Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain i residue 47 SER Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain u residue 47 SER Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 242 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 233 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 266 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 307 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 21 HIS h 68 HIS ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 43839 Z= 0.387 Angle : 0.874 16.515 60339 Z= 0.346 Chirality : 0.043 0.166 5920 Planarity : 0.006 0.065 7401 Dihedral : 16.467 179.812 7619 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.17 % Allowed : 11.93 % Favored : 85.90 % 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: 1.85 (0.12), residues: 4222 helix: 2.12 (0.09), residues: 2888 sheet: -0.89 (0.70), residues: 48 loop : -0.78 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 8 HIS 0.015 0.002 HIS m 182 PHE 0.023 0.002 PHE k 23 TYR 0.027 0.002 TYR G 24 ARG 0.011 0.001 ARG J 46 *********************** 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 613 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 534 time to evaluate : 4.389 Fit side-chains revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7439 (pm20) REVERT: H 81 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.4454 (mm-30) REVERT: H 159 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.5859 (tp30) REVERT: B 19 GLU cc_start: 0.6970 (tt0) cc_final: 0.6764 (tt0) REVERT: F 3 LYS cc_start: 0.7858 (mtpp) cc_final: 0.7324 (mptt) REVERT: S 33 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8526 (mp) REVERT: T 12 LEU cc_start: 0.5821 (mp) cc_final: 0.5341 (pt) REVERT: W 26 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6750 (tp) REVERT: 0 15 GLU cc_start: 0.6701 (pm20) cc_final: 0.6447 (pm20) REVERT: m 233 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7998 (mtp-110) REVERT: h 160 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7575 (mp) REVERT: h 170 ASP cc_start: 0.7212 (t0) cc_final: 0.6885 (t0) REVERT: h 191 LEU cc_start: 0.8569 (mt) cc_final: 0.8273 (mt) REVERT: h 197 LYS cc_start: 0.8138 (tptp) cc_final: 0.7717 (tttt) REVERT: h 231 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: k 1 MET cc_start: 0.6341 (tmm) cc_final: 0.5772 (tmm) REVERT: q 9 MET cc_start: 0.6395 (mtm) cc_final: 0.6084 (mpp) REVERT: s 9 MET cc_start: 0.5729 (mtm) cc_final: 0.5330 (mtp) REVERT: x 25 MET cc_start: 0.4757 (tpp) cc_final: 0.4326 (ttt) REVERT: z 25 MET cc_start: 0.2011 (mtm) cc_final: 0.1737 (tmm) REVERT: c 58 GLN cc_start: 0.7404 (tp40) cc_final: 0.7138 (tp-100) outliers start: 79 outliers final: 56 residues processed: 583 average time/residue: 0.5051 time to fit residues: 492.6660 Evaluate side-chains 586 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 523 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 9 residue 54 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain m residue 279 THR Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 160 ILE Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 211 ASP Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 228 LEU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain a residue 45 GLU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain i residue 47 SER Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 37 SER Chi-restraints excluded: chain t residue 40 LEU Chi-restraints excluded: chain u residue 47 SER Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain 5 residue 30 MET Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 355 optimal weight: 0.0980 chunk 374 optimal weight: 7.9990 chunk 342 optimal weight: 8.9990 chunk 364 optimal weight: 5.9990 chunk 219 optimal weight: 0.5980 chunk 158 optimal weight: 9.9990 chunk 286 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 329 optimal weight: 1.9990 chunk 344 optimal weight: 7.9990 chunk 363 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 20 GLN C 66 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 43839 Z= 0.224 Angle : 0.734 15.176 60339 Z= 0.288 Chirality : 0.038 0.155 5920 Planarity : 0.005 0.065 7401 Dihedral : 15.929 179.232 7619 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.03 % Allowed : 12.29 % Favored : 85.68 % 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: 2.20 (0.13), residues: 4222 helix: 2.41 (0.09), residues: 2878 sheet: -0.66 (0.72), residues: 48 loop : -0.70 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Q 8 HIS 0.012 0.001 HIS l 153 PHE 0.022 0.002 PHE k 23 TYR 0.018 0.001 TYR F 41 ARG 0.007 0.000 ARG J 46 *********************** 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 621 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 547 time to evaluate : 4.416 Fit side-chains revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7482 (pm20) REVERT: H 81 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.4532 (mm-30) REVERT: H 159 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.5946 (tp30) REVERT: B 19 GLU cc_start: 0.6894 (tt0) cc_final: 0.6686 (tt0) REVERT: F 3 LYS cc_start: 0.7844 (mtpp) cc_final: 0.7300 (mptt) REVERT: S 33 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8435 (mp) REVERT: T 12 LEU cc_start: 0.5688 (mp) cc_final: 0.5171 (pt) REVERT: W 26 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6729 (tp) REVERT: Y 30 MET cc_start: 0.3649 (OUTLIER) cc_final: 0.3014 (mmt) REVERT: 0 15 GLU cc_start: 0.6628 (pm20) cc_final: 0.6385 (pm20) REVERT: h 160 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7499 (mp) REVERT: h 170 ASP cc_start: 0.7105 (t0) cc_final: 0.6693 (t0) REVERT: h 191 LEU cc_start: 0.8574 (mt) cc_final: 0.8284 (mt) REVERT: h 197 LYS cc_start: 0.8103 (tptp) cc_final: 0.7657 (tttt) REVERT: h 231 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: k 1 MET cc_start: 0.6342 (tmm) cc_final: 0.5711 (tmm) REVERT: q 9 MET cc_start: 0.6406 (mtm) cc_final: 0.6130 (mpp) REVERT: s 8 TRP cc_start: 0.5621 (m100) cc_final: 0.4915 (m100) REVERT: s 9 MET cc_start: 0.5751 (mtm) cc_final: 0.5238 (mtp) REVERT: x 25 MET cc_start: 0.4785 (tpp) cc_final: 0.4401 (ttt) REVERT: c 58 GLN cc_start: 0.7436 (tp40) cc_final: 0.7125 (tp-100) outliers start: 74 outliers final: 60 residues processed: 592 average time/residue: 0.5000 time to fit residues: 494.7948 Evaluate side-chains 603 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 535 time to evaluate : 4.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 23 PHE Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 9 residue 54 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain m residue 279 THR Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 160 ILE Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 211 ASP Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 228 LEU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain i residue 47 SER Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain n residue 20 LEU Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain u residue 47 SER Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain 5 residue 30 MET Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain 3 residue 30 MET Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 60 ASN Chi-restraints excluded: chain c residue 66 ASN Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 239 optimal weight: 0.9980 chunk 385 optimal weight: 0.9990 chunk 235 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 404 optimal weight: 7.9990 chunk 372 optimal weight: 3.9990 chunk 322 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 5 ASN H 35 ASN 7 20 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 HIS ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 66 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 43839 Z= 0.201 Angle : 0.718 14.010 60339 Z= 0.281 Chirality : 0.037 0.150 5920 Planarity : 0.005 0.064 7401 Dihedral : 15.733 179.234 7619 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.98 % Allowed : 12.53 % Favored : 85.49 % 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: 2.34 (0.13), residues: 4222 helix: 2.50 (0.09), residues: 2884 sheet: -0.59 (0.73), residues: 48 loop : -0.63 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Q 8 HIS 0.011 0.001 HIS m 182 PHE 0.021 0.001 PHE k 23 TYR 0.018 0.001 TYR q 41 ARG 0.006 0.000 ARG J 46 ********************** 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 611 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 539 time to evaluate : 4.004 Fit side-chains revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: H 81 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.4528 (mm-30) REVERT: H 159 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.5985 (tp30) REVERT: B 19 GLU cc_start: 0.6891 (tt0) cc_final: 0.6679 (tt0) REVERT: F 3 LYS cc_start: 0.7820 (mtpp) cc_final: 0.7301 (mptt) REVERT: S 33 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8437 (mp) REVERT: T 12 LEU cc_start: 0.5785 (mp) cc_final: 0.5134 (pt) REVERT: W 26 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6723 (tp) REVERT: Y 30 MET cc_start: 0.3611 (OUTLIER) cc_final: 0.3001 (mmt) REVERT: 7 3 LYS cc_start: 0.8064 (tttt) cc_final: 0.7853 (tptt) REVERT: 0 15 GLU cc_start: 0.6586 (pm20) cc_final: 0.6319 (pm20) REVERT: h 160 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7464 (mp) REVERT: h 170 ASP cc_start: 0.7070 (t0) cc_final: 0.6671 (t0) REVERT: h 191 LEU cc_start: 0.8535 (mt) cc_final: 0.8248 (mt) REVERT: h 197 LYS cc_start: 0.8096 (tptp) cc_final: 0.7648 (tttt) REVERT: h 231 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: k 1 MET cc_start: 0.6305 (tmm) cc_final: 0.5667 (tmm) REVERT: q 9 MET cc_start: 0.6350 (mtm) cc_final: 0.6113 (mpp) REVERT: s 8 TRP cc_start: 0.5591 (m100) cc_final: 0.4885 (m100) REVERT: s 9 MET cc_start: 0.5753 (mtm) cc_final: 0.5249 (mtp) REVERT: x 25 MET cc_start: 0.4653 (tpp) cc_final: 0.4219 (ttt) REVERT: z 25 MET cc_start: 0.3317 (tmm) cc_final: 0.2357 (mtm) REVERT: c 58 GLN cc_start: 0.7395 (tp40) cc_final: 0.7111 (tp-100) outliers start: 72 outliers final: 62 residues processed: 582 average time/residue: 0.4849 time to fit residues: 474.2834 Evaluate side-chains 602 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 532 time to evaluate : 3.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 23 PHE Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 9 residue 54 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 204 LYS Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain m residue 279 THR Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 160 ILE Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 211 ASP Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 228 LEU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain i residue 47 SER Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain n residue 20 LEU Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain u residue 47 SER Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain 5 residue 30 MET Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain 3 residue 30 MET Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 60 ASN Chi-restraints excluded: chain c residue 66 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 255 optimal weight: 2.9990 chunk 343 optimal weight: 0.1980 chunk 98 optimal weight: 10.0000 chunk 296 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 322 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 331 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 5 ASN E 18 GLN 7 20 GLN C 66 ASN h 68 HIS ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.167531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.137571 restraints weight = 45766.049| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.58 r_work: 0.3145 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 43839 Z= 0.209 Angle : 0.720 14.012 60339 Z= 0.282 Chirality : 0.037 0.148 5920 Planarity : 0.005 0.064 7401 Dihedral : 15.615 179.184 7619 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.03 % Allowed : 12.59 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.13), residues: 4222 helix: 2.52 (0.09), residues: 2884 sheet: -0.53 (0.74), residues: 48 loop : -0.61 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 157 HIS 0.011 0.001 HIS l 153 PHE 0.019 0.001 PHE m 67 TYR 0.018 0.001 TYR q 41 ARG 0.006 0.000 ARG J 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9571.60 seconds wall clock time: 172 minutes 27.66 seconds (10347.66 seconds total)