Starting phenix.real_space_refine (version: dev) on Wed May 18 07:41:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/05_2022/6h3c_0132.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/05_2022/6h3c_0132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/05_2022/6h3c_0132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/05_2022/6h3c_0132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/05_2022/6h3c_0132.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/05_2022/6h3c_0132.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 242": "OE1" <-> "OE2" Residue "H PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 49982 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4134 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 5, 'TRANS': 249} Chain: "B" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4122 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 2 Chain: "C" Number of atoms: 6077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6077 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 354} Chain: "D" Number of atoms: 3761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3761 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 15, 'TRANS': 220, 'PCIS': 1} Chain: "F" Number of atoms: 4134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4134 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 5, 'TRANS': 249} Chain: "G" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4122 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 2 Chain: "H" Number of atoms: 6077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6077 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 354} Chain: "I" Number of atoms: 3761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3761 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 15, 'TRANS': 220, 'PCIS': 1} Chain: "E" Number of atoms: 6893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6893 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 21, 'TRANS': 417, 'PCIS': 1} Chain breaks: 1 Chain: "J" Number of atoms: 6893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6893 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 21, 'TRANS': 417, 'PCIS': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 22.42, per 1000 atoms: 0.45 Number of scatterers: 49982 At special positions: 0 Unit cell: (165.98, 181.46, 149.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 136 16.00 O 4708 8.00 N 4334 7.00 C 15942 6.00 H 24860 1.00 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=0, symmetry=0 Time building additional restraints: 42.57 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 122 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 124 " pdb=" ZN G 401 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 122 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 124 " 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5980 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 24 sheets defined 45.7% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 removed outlier: 3.504A pdb=" N ASN A 19 " --> pdb=" O PHE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.543A pdb=" N ARG A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 182 through 192 removed outlier: 3.526A pdb=" N LYS A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 203 through 255 removed outlier: 3.613A pdb=" N ARG A 207 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 93 through 112 Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 234 through 252 removed outlier: 3.521A pdb=" N CYS B 240 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 279 Processing helix chain 'B' and resid 279 through 316 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 14 through 24 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 112 through 133 removed outlier: 3.537A pdb=" N ARG C 131 " --> pdb=" O PHE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 4.017A pdb=" N THR C 144 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 154 removed outlier: 3.575A pdb=" N GLU C 153 " --> pdb=" O GLN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 231 through 234 Processing helix chain 'C' and resid 245 through 280 Proline residue: C 251 - end of helix removed outlier: 5.109A pdb=" N HIS C 255 " --> pdb=" O PRO C 251 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU C 273 " --> pdb=" O HIS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 377 Proline residue: C 371 - end of helix Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 119 through 135 Processing helix chain 'D' and resid 162 through 171 removed outlier: 3.686A pdb=" N LEU D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR D 171 " --> pdb=" O CYS D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 192 Processing helix chain 'D' and resid 229 through 238 removed outlier: 5.620A pdb=" N MET D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.604A pdb=" N GLU D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 269 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 287 through 292 Processing helix chain 'D' and resid 292 through 299 Processing helix chain 'D' and resid 307 through 311 Processing helix chain 'F' and resid 6 through 19 removed outlier: 3.503A pdb=" N ASN F 19 " --> pdb=" O PHE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 85 Processing helix chain 'F' and resid 106 through 120 removed outlier: 3.544A pdb=" N ARG F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 168 Processing helix chain 'F' and resid 182 through 192 removed outlier: 3.526A pdb=" N LYS F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 196 Processing helix chain 'F' and resid 203 through 255 removed outlier: 3.614A pdb=" N ARG F 207 " --> pdb=" O MET F 203 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR F 213 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU F 216 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 27 Processing helix chain 'G' and resid 93 through 112 Processing helix chain 'G' and resid 132 through 146 Processing helix chain 'G' and resid 225 through 232 Processing helix chain 'G' and resid 234 through 252 removed outlier: 3.521A pdb=" N CYS G 240 " --> pdb=" O PRO G 236 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU G 243 " --> pdb=" O LEU G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 279 Processing helix chain 'G' and resid 279 through 316 Processing helix chain 'H' and resid 2 through 9 Processing helix chain 'H' and resid 14 through 24 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 99 through 104 Processing helix chain 'H' and resid 109 through 111 No H-bonds generated for 'chain 'H' and resid 109 through 111' Processing helix chain 'H' and resid 112 through 133 removed outlier: 3.538A pdb=" N ARG H 131 " --> pdb=" O PHE H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 147 removed outlier: 4.018A pdb=" N THR H 144 " --> pdb=" O PHE H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 154 removed outlier: 3.576A pdb=" N GLU H 153 " --> pdb=" O GLN H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 230 Processing helix chain 'H' and resid 231 through 234 Processing helix chain 'H' and resid 245 through 280 Proline residue: H 251 - end of helix removed outlier: 5.110A pdb=" N HIS H 255 " --> pdb=" O PRO H 251 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU H 273 " --> pdb=" O HIS H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 377 Proline residue: H 371 - end of helix Processing helix chain 'I' and resid 102 through 107 Processing helix chain 'I' and resid 119 through 135 Processing helix chain 'I' and resid 162 through 171 removed outlier: 3.687A pdb=" N LEU I 166 " --> pdb=" O ASP I 162 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR I 171 " --> pdb=" O CYS I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 192 Processing helix chain 'I' and resid 229 through 238 removed outlier: 5.620A pdb=" N MET I 235 " --> pdb=" O PRO I 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 255 removed outlier: 3.604A pdb=" N GLU I 254 " --> pdb=" O ASN I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 269 Processing helix chain 'I' and resid 270 through 272 No H-bonds generated for 'chain 'I' and resid 270 through 272' Processing helix chain 'I' and resid 287 through 292 Processing helix chain 'I' and resid 292 through 299 Processing helix chain 'I' and resid 307 through 311 Processing helix chain 'E' and resid 27 through 32 Processing helix chain 'E' and resid 32 through 48 Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'E' and resid 69 through 74 Processing helix chain 'E' and resid 88 through 105 removed outlier: 3.770A pdb=" N LEU E 103 " --> pdb=" O GLN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 134 Processing helix chain 'E' and resid 184 through 196 Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 234 through 240 Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 296 through 298 No H-bonds generated for 'chain 'E' and resid 296 through 298' Processing helix chain 'E' and resid 307 through 322 Processing helix chain 'E' and resid 323 through 347 Processing helix chain 'E' and resid 353 through 355 No H-bonds generated for 'chain 'E' and resid 353 through 355' Processing helix chain 'E' and resid 366 through 369 Processing helix chain 'E' and resid 371 through 381 removed outlier: 4.645A pdb=" N ARG E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 416 through 439 removed outlier: 3.585A pdb=" N ILE E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 454 removed outlier: 4.307A pdb=" N SER E 449 " --> pdb=" O GLN E 445 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU E 452 " --> pdb=" O LYS E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 473 Processing helix chain 'J' and resid 27 through 32 Processing helix chain 'J' and resid 32 through 48 Processing helix chain 'J' and resid 60 through 68 Processing helix chain 'J' and resid 69 through 74 Processing helix chain 'J' and resid 88 through 105 removed outlier: 3.770A pdb=" N LEU J 103 " --> pdb=" O GLN J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 134 Processing helix chain 'J' and resid 184 through 196 Processing helix chain 'J' and resid 212 through 223 Processing helix chain 'J' and resid 234 through 240 Processing helix chain 'J' and resid 245 through 249 Processing helix chain 'J' and resid 290 through 295 Processing helix chain 'J' and resid 296 through 298 No H-bonds generated for 'chain 'J' and resid 296 through 298' Processing helix chain 'J' and resid 307 through 322 Processing helix chain 'J' and resid 323 through 347 Processing helix chain 'J' and resid 353 through 355 No H-bonds generated for 'chain 'J' and resid 353 through 355' Processing helix chain 'J' and resid 366 through 369 Processing helix chain 'J' and resid 371 through 381 removed outlier: 4.645A pdb=" N ARG J 377 " --> pdb=" O ALA J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 412 Processing helix chain 'J' and resid 416 through 439 removed outlier: 3.585A pdb=" N ILE J 433 " --> pdb=" O GLU J 429 " (cutoff:3.500A) Processing helix chain 'J' and resid 443 through 454 removed outlier: 4.307A pdb=" N SER J 449 " --> pdb=" O GLN J 445 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU J 452 " --> pdb=" O LYS J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 454 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 157 removed outlier: 3.536A pdb=" N GLN A 156 " --> pdb=" O ARG A 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 161 removed outlier: 6.736A pdb=" N ALA A 3 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA A 2 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE A 56 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER A 4 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ASN A 58 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A 29 " --> pdb=" O HIS A 57 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS A 59 " --> pdb=" O PHE A 27 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE A 27 " --> pdb=" O HIS A 59 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU A 25 " --> pdb=" O PRO A 61 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP A 94 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N PHE A 130 " --> pdb=" O TRP A 94 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG A 96 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE A 132 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ARG A 98 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N SER A 134 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARG B 167 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE B 157 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL B 117 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLY B 40 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY B 119 " --> pdb=" O CYS B 38 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 37 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL B 77 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE B 39 " --> pdb=" O HIS B 75 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER B 76 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 12 " --> pdb=" O HIS B 217 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL B 219 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 14 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 70 removed outlier: 3.510A pdb=" N LYS A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 36 through 41 removed outlier: 4.755A pdb=" N LEU C 40 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ARG C 55 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AA6, first strand: chain 'C' and resid 286 through 288 removed outlier: 6.778A pdb=" N THR C 298 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 297 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 325 " --> pdb=" O GLN C 344 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR C 340 " --> pdb=" O SER C 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 155 through 160 removed outlier: 4.310A pdb=" N GLY D 158 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE D 144 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 143 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS D 94 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL D 216 " --> pdb=" O CYS D 98 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N TYR D 280 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL D 245 " --> pdb=" O TYR D 280 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL D 282 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR D 247 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AA9, first strand: chain 'F' and resid 154 through 157 removed outlier: 3.537A pdb=" N GLN F 156 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 160 through 161 removed outlier: 6.735A pdb=" N ALA F 3 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA F 2 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE F 56 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER F 4 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ASN F 58 " --> pdb=" O SER F 4 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU F 29 " --> pdb=" O HIS F 57 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS F 59 " --> pdb=" O PHE F 27 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE F 27 " --> pdb=" O HIS F 59 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU F 25 " --> pdb=" O PRO F 61 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP F 94 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N PHE F 130 " --> pdb=" O TRP F 94 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG F 96 " --> pdb=" O PHE F 130 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE F 132 " --> pdb=" O ARG F 96 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ARG F 98 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N SER F 134 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARG G 167 " --> pdb=" O PHE G 157 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE G 157 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL G 117 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLY G 40 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY G 119 " --> pdb=" O CYS G 38 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU G 37 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL G 77 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE G 39 " --> pdb=" O HIS G 75 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER G 76 " --> pdb=" O GLU G 15 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL G 12 " --> pdb=" O HIS G 217 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL G 219 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU G 14 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 69 through 70 removed outlier: 3.510A pdb=" N LYS F 74 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 36 through 41 removed outlier: 4.754A pdb=" N LEU H 40 " --> pdb=" O ARG H 55 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ARG H 55 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 156 through 159 Processing sheet with id=AB5, first strand: chain 'H' and resid 286 through 288 removed outlier: 6.779A pdb=" N THR H 298 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU H 297 " --> pdb=" O ILE H 312 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 325 " --> pdb=" O GLN H 344 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR H 340 " --> pdb=" O SER H 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 155 through 160 removed outlier: 4.310A pdb=" N GLY I 158 " --> pdb=" O PHE I 144 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE I 144 " --> pdb=" O GLY I 158 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU I 143 " --> pdb=" O GLU I 93 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS I 94 " --> pdb=" O VAL I 210 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL I 216 " --> pdb=" O CYS I 98 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N TYR I 280 " --> pdb=" O PHE I 243 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL I 245 " --> pdb=" O TYR I 280 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL I 282 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR I 247 " --> pdb=" O VAL I 282 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 110 through 111 Processing sheet with id=AB8, first strand: chain 'E' and resid 50 through 51 removed outlier: 6.972A pdb=" N LEU E 50 " --> pdb=" O THR E 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 113 through 116 removed outlier: 6.408A pdb=" N LEU E 227 " --> pdb=" O ILE E 252 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR E 254 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA E 229 " --> pdb=" O THR E 254 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N THR E 256 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 275 through 278 Processing sheet with id=AC2, first strand: chain 'E' and resid 350 through 351 removed outlier: 4.021A pdb=" N SER E 350 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 50 through 51 removed outlier: 6.971A pdb=" N LEU J 50 " --> pdb=" O THR J 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'J' and resid 113 through 116 removed outlier: 6.408A pdb=" N LEU J 227 " --> pdb=" O ILE J 252 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR J 254 " --> pdb=" O LEU J 227 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA J 229 " --> pdb=" O THR J 254 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR J 256 " --> pdb=" O ALA J 229 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 275 through 278 Processing sheet with id=AC6, first strand: chain 'J' and resid 350 through 351 removed outlier: 4.020A pdb=" N SER J 350 " --> pdb=" O ASP J 364 " (cutoff:3.500A) 1249 hydrogen bonds defined for protein. 3507 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: 19.53 Time building geometry restraints manager: 44.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 24790 1.04 - 1.24: 4081 1.24 - 1.44: 7957 1.44 - 1.64: 13502 1.64 - 1.85: 202 Bond restraints: 50532 Sorted by residual: bond pdb=" CB HIS E 359 " pdb=" CG HIS E 359 " ideal model delta sigma weight residual 1.497 1.382 0.115 1.40e-02 5.10e+03 6.72e+01 bond pdb=" CB HIS J 359 " pdb=" CG HIS J 359 " ideal model delta sigma weight residual 1.497 1.382 0.115 1.40e-02 5.10e+03 6.72e+01 bond pdb=" CB HIS G 122 " pdb=" CG HIS G 122 " ideal model delta sigma weight residual 1.497 1.394 0.103 1.40e-02 5.10e+03 5.37e+01 bond pdb=" CB HIS B 122 " pdb=" CG HIS B 122 " ideal model delta sigma weight residual 1.497 1.395 0.102 1.40e-02 5.10e+03 5.28e+01 bond pdb=" CA PRO I 220 " pdb=" C PRO I 220 " ideal model delta sigma weight residual 1.514 1.551 -0.036 5.50e-03 3.31e+04 4.34e+01 ... (remaining 50527 not shown) Histogram of bond angle deviations from ideal: 93.57 - 101.68: 72 101.68 - 109.79: 38747 109.79 - 117.89: 28931 117.89 - 126.00: 22642 126.00 - 134.11: 874 Bond angle restraints: 91266 Sorted by residual: angle pdb=" N GLU B 210 " pdb=" CA GLU B 210 " pdb=" C GLU B 210 " ideal model delta sigma weight residual 113.20 124.14 -10.94 1.21e+00 6.83e-01 8.17e+01 angle pdb=" N GLU G 210 " pdb=" CA GLU G 210 " pdb=" C GLU G 210 " ideal model delta sigma weight residual 113.20 124.12 -10.92 1.21e+00 6.83e-01 8.14e+01 angle pdb=" N SER H 42 " pdb=" CA SER H 42 " pdb=" C SER H 42 " ideal model delta sigma weight residual 111.71 121.91 -10.20 1.15e+00 7.56e-01 7.86e+01 angle pdb=" N SER C 42 " pdb=" CA SER C 42 " pdb=" C SER C 42 " ideal model delta sigma weight residual 111.71 121.90 -10.19 1.15e+00 7.56e-01 7.85e+01 angle pdb=" CA HIS I 249 " pdb=" CB HIS I 249 " pdb=" CG HIS I 249 " ideal model delta sigma weight residual 113.80 122.65 -8.85 1.00e+00 1.00e+00 7.84e+01 ... (remaining 91261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 19589 16.86 - 33.73: 643 33.73 - 50.59: 117 50.59 - 67.46: 67 67.46 - 84.32: 30 Dihedral angle restraints: 20446 sinusoidal: 9564 harmonic: 10882 Sorted by residual: dihedral pdb=" C TYR I 240 " pdb=" N TYR I 240 " pdb=" CA TYR I 240 " pdb=" CB TYR I 240 " ideal model delta harmonic sigma weight residual -122.60 -112.33 -10.27 0 2.50e+00 1.60e-01 1.69e+01 dihedral pdb=" C TYR D 240 " pdb=" N TYR D 240 " pdb=" CA TYR D 240 " pdb=" CB TYR D 240 " ideal model delta harmonic sigma weight residual -122.60 -112.35 -10.25 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" N PHE C 73 " pdb=" C PHE C 73 " pdb=" CA PHE C 73 " pdb=" CB PHE C 73 " ideal model delta harmonic sigma weight residual 122.80 132.23 -9.43 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 20443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2801 0.104 - 0.209: 868 0.209 - 0.313: 159 0.313 - 0.418: 10 0.418 - 0.522: 4 Chirality restraints: 3842 Sorted by residual: chirality pdb=" CA PHE C 73 " pdb=" N PHE C 73 " pdb=" C PHE C 73 " pdb=" CB PHE C 73 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" CA PHE H 73 " pdb=" N PHE H 73 " pdb=" C PHE H 73 " pdb=" CB PHE H 73 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" CA SER I 102 " pdb=" N SER I 102 " pdb=" C SER I 102 " pdb=" CB SER I 102 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 ... (remaining 3839 not shown) Planarity restraints: 7496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 316 " 0.041 2.00e-02 2.50e+03 8.34e-02 6.95e+01 pdb=" C GLU G 316 " -0.144 2.00e-02 2.50e+03 pdb=" O GLU G 316 " 0.052 2.00e-02 2.50e+03 pdb=" OXT GLU G 316 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 316 " -0.041 2.00e-02 2.50e+03 8.32e-02 6.92e+01 pdb=" C GLU B 316 " 0.144 2.00e-02 2.50e+03 pdb=" O GLU B 316 " -0.052 2.00e-02 2.50e+03 pdb=" OXT GLU B 316 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 240 " -0.093 2.00e-02 2.50e+03 4.09e-02 5.02e+01 pdb=" CG TYR I 240 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR I 240 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR I 240 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR I 240 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR I 240 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR I 240 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 240 " -0.076 2.00e-02 2.50e+03 pdb=" HD1 TYR I 240 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR I 240 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR I 240 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR I 240 " 0.003 2.00e-02 2.50e+03 ... (remaining 7493 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1983 2.15 - 2.77: 99431 2.77 - 3.38: 145524 3.38 - 3.99: 191440 3.99 - 4.60: 300410 Nonbonded interactions: 738788 Sorted by model distance: nonbonded pdb=" H ARG H 224 " pdb=" H ILE H 225 " model vdw 1.542 2.100 nonbonded pdb=" H ARG C 224 " pdb=" H ILE C 225 " model vdw 1.542 2.100 nonbonded pdb=" H GLY E 393 " pdb=" H ASP E 394 " model vdw 1.577 2.100 nonbonded pdb=" H GLY J 393 " pdb=" H ASP J 394 " model vdw 1.578 2.100 nonbonded pdb=" H THR G 163 " pdb=" H LYS G 164 " model vdw 1.636 2.100 ... (remaining 738783 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 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 136 5.16 5 C 15942 2.51 5 N 4334 2.21 5 O 4708 1.98 5 H 24860 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.730 Extract box with map and model: 13.110 Check model and map are aligned: 0.710 Convert atoms to be neutral: 0.400 Process input model: 162.700 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 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 0.142 25672 Z= 1.323 Angle : 1.861 15.244 34764 Z= 1.261 Chirality : 0.100 0.522 3842 Planarity : 0.009 0.083 4526 Dihedral : 10.539 84.319 9598 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.33 % Favored : 94.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3114 helix: 0.10 (0.14), residues: 1244 sheet: 0.31 (0.24), residues: 456 loop : -0.63 (0.17), residues: 1414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 720 time to evaluate : 3.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 720 average time/residue: 0.8435 time to fit residues: 933.2997 Evaluate side-chains 417 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 4.262 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 0.5980 chunk 234 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 158 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 242 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 180 optimal weight: 20.0000 chunk 281 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN C 100 GLN C 338 GLN ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN H 100 GLN ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 338 GLN ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 GLN E 336 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 25672 Z= 0.261 Angle : 0.793 9.227 34764 Z= 0.439 Chirality : 0.045 0.218 3842 Planarity : 0.006 0.131 4526 Dihedral : 6.023 76.615 3424 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.91 % Favored : 94.70 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 3114 helix: 0.42 (0.14), residues: 1256 sheet: -0.00 (0.23), residues: 472 loop : -1.07 (0.16), residues: 1386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 457 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 42 residues processed: 496 average time/residue: 0.7670 time to fit residues: 616.7166 Evaluate side-chains 417 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 375 time to evaluate : 3.868 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 42 outliers final: 1 residues processed: 42 average time/residue: 0.5839 time to fit residues: 48.7184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 282 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 303 GLN D 136 HIS F 155 ASN ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 HIS G 177 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN G 303 GLN J 332 GLN J 336 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 25672 Z= 0.320 Angle : 0.718 8.682 34764 Z= 0.392 Chirality : 0.043 0.181 3842 Planarity : 0.006 0.101 4526 Dihedral : 5.968 83.458 3424 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.13 % Favored : 93.45 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3114 helix: 0.42 (0.14), residues: 1256 sheet: -0.31 (0.23), residues: 486 loop : -1.33 (0.16), residues: 1372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 382 time to evaluate : 4.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 400 average time/residue: 0.7933 time to fit residues: 521.0262 Evaluate side-chains 348 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 332 time to evaluate : 4.015 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.5411 time to fit residues: 21.1659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 3.9990 chunk 212 optimal weight: 20.0000 chunk 146 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 189 optimal weight: 20.0000 chunk 283 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 268 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 25672 Z= 0.206 Angle : 0.624 8.070 34764 Z= 0.337 Chirality : 0.041 0.164 3842 Planarity : 0.005 0.078 4526 Dihedral : 5.843 89.584 3424 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.78 % Favored : 93.77 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3114 helix: 0.62 (0.14), residues: 1270 sheet: -0.39 (0.23), residues: 482 loop : -1.42 (0.16), residues: 1362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 363 time to evaluate : 4.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 378 average time/residue: 0.7688 time to fit residues: 466.8480 Evaluate side-chains 347 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 327 time to evaluate : 4.340 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 20 average time/residue: 0.5481 time to fit residues: 24.9636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 268 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 ASN J 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.150 25672 Z= 0.742 Angle : 0.800 86.332 34764 Z= 0.384 Chirality : 0.041 0.274 3842 Planarity : 0.005 0.081 4526 Dihedral : 5.705 84.377 3424 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.62 % Favored : 92.94 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3114 helix: 0.77 (0.14), residues: 1258 sheet: -0.43 (0.23), residues: 482 loop : -1.55 (0.16), residues: 1374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 349 time to evaluate : 4.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 360 average time/residue: 0.8149 time to fit residues: 474.2755 Evaluate side-chains 352 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 339 time to evaluate : 4.033 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.5682 time to fit residues: 18.7421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 299 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 HIS B 244 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.231 25672 Z= 0.517 Angle : 0.779 15.542 34764 Z= 0.423 Chirality : 0.045 0.190 3842 Planarity : 0.006 0.083 4526 Dihedral : 5.922 75.169 3424 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.35 % Favored : 92.20 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.35 (0.14), residues: 3114 helix: 0.25 (0.14), residues: 1276 sheet: -0.99 (0.23), residues: 456 loop : -1.96 (0.15), residues: 1382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 338 time to evaluate : 4.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 28 residues processed: 363 average time/residue: 0.8054 time to fit residues: 463.0173 Evaluate side-chains 331 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 303 time to evaluate : 4.074 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.6245 time to fit residues: 35.2915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 219 optimal weight: 7.9990 chunk 169 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 HIS ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.193 25672 Z= 0.246 Angle : 0.639 12.895 34764 Z= 0.342 Chirality : 0.041 0.162 3842 Planarity : 0.005 0.079 4526 Dihedral : 5.675 71.086 3424 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.13 % Favored : 93.42 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.00 (0.15), residues: 3114 helix: 0.62 (0.14), residues: 1270 sheet: -0.83 (0.23), residues: 448 loop : -1.83 (0.16), residues: 1396 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 330 time to evaluate : 4.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 338 average time/residue: 0.8148 time to fit residues: 441.5115 Evaluate side-chains 326 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 308 time to evaluate : 3.997 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.5434 time to fit residues: 23.4719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 178 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 58 optimal weight: 0.2980 chunk 57 optimal weight: 0.5980 chunk 189 optimal weight: 30.0000 chunk 203 optimal weight: 9.9990 chunk 147 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.289 25672 Z= 0.215 Angle : 0.624 19.864 34764 Z= 0.332 Chirality : 0.041 0.182 3842 Planarity : 0.005 0.083 4526 Dihedral : 5.477 67.053 3424 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.65 % Favored : 93.00 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3114 helix: 0.81 (0.14), residues: 1276 sheet: -0.71 (0.24), residues: 442 loop : -1.78 (0.16), residues: 1396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 321 time to evaluate : 4.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 324 average time/residue: 0.8445 time to fit residues: 438.7505 Evaluate side-chains 314 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 310 time to evaluate : 4.246 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.6995 time to fit residues: 10.1256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 0.6980 chunk 286 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 218 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 251 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 277 optimal weight: 0.0030 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.606 25672 Z= 0.323 Angle : 0.754 72.536 34764 Z= 0.370 Chirality : 0.041 0.164 3842 Planarity : 0.005 0.110 4526 Dihedral : 5.437 64.084 3424 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.00 % Favored : 92.58 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 3114 helix: 0.89 (0.14), residues: 1272 sheet: -0.77 (0.23), residues: 442 loop : -1.80 (0.16), residues: 1400 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 312 time to evaluate : 3.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 315 average time/residue: 0.8174 time to fit residues: 413.0184 Evaluate side-chains 313 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 306 time to evaluate : 3.973 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6144 time to fit residues: 12.7923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 chunk 308 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.506 25672 Z= 0.333 Angle : 0.723 48.829 34764 Z= 0.376 Chirality : 0.041 0.234 3842 Planarity : 0.005 0.132 4526 Dihedral : 5.394 59.748 3424 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.97 % Favored : 92.65 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 3114 helix: 0.87 (0.14), residues: 1274 sheet: -0.81 (0.24), residues: 438 loop : -1.84 (0.16), residues: 1402 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 306 time to evaluate : 3.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 308 average time/residue: 0.8064 time to fit residues: 395.3494 Evaluate side-chains 301 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 299 time to evaluate : 3.957 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6920 time to fit residues: 7.1468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 9.9990 chunk 261 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 226 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 246 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.177586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.135661 restraints weight = 154053.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.134446 restraints weight = 86483.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.135175 restraints weight = 62726.587| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.483 25672 Z= 0.366 Angle : 0.822 73.900 34764 Z= 0.408 Chirality : 0.041 0.245 3842 Planarity : 0.005 0.068 4526 Dihedral : 5.403 59.709 3424 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.13 % Favored : 92.49 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3114 helix: 0.87 (0.14), residues: 1274 sheet: -0.81 (0.24), residues: 438 loop : -1.84 (0.16), residues: 1402 =============================================================================== Job complete usr+sys time: 10396.71 seconds wall clock time: 185 minutes 27.95 seconds (11127.95 seconds total)