Starting phenix.real_space_refine (version: dev) on Thu Dec 15 14:42:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te0_10473/12_2022/6te0_10473_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te0_10473/12_2022/6te0_10473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te0_10473/12_2022/6te0_10473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te0_10473/12_2022/6te0_10473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te0_10473/12_2022/6te0_10473_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te0_10473/12_2022/6te0_10473_trim_updated.pdb" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 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 "C ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 179": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 418": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 223": "OD1" <-> "OD2" Residue "M ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 79188 Number of models: 1 Model: "" Number of chains: 29 Chain: "C" Number of atoms: 8317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 8317 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 506} Chain breaks: 1 Chain: "A" Number of atoms: 8292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 8292 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 504} Chain breaks: 1 Chain: "B" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 8336 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 508} Chain breaks: 1 Chain: "F" Number of atoms: 7408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7408 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 465} Chain: "D" Number of atoms: 7408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7408 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 466} Chain: "E" Number of atoms: 7407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7407 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 465} Chain: "L" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2596 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "J" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2596 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "K" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2596 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "M" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3778 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 14, 'TRANS': 228} Chain: "G" Number of atoms: 4898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 4898 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 5, 'TRANS': 297} Chain: "H" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2448 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "I" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1077 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "O" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "P" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "Q" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "R" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "S" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "T" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "U" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "V" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "W" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "X" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'TRT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 28.09, per 1000 atoms: 0.35 Number of scatterers: 79188 At special positions: 0 Unit cell: (165.9, 166.95, 233.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 233 16.00 P 14 15.00 Mg 5 11.99 O 7457 8.00 N 6559 7.00 C 25085 6.00 H 39835 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: 55.35 Conformation dependent library (CDL) restraints added in 6.0 seconds 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9466 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 212 helices and 27 sheets defined 47.7% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 190 through 201 removed outlier: 3.723A pdb=" N ALA C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 207 removed outlier: 3.856A pdb=" N GLU C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 203 through 207' Processing helix chain 'C' and resid 225 through 237 Processing helix chain 'C' and resid 241 through 243 No H-bonds generated for 'chain 'C' and resid 241 through 243' Processing helix chain 'C' and resid 255 through 258 No H-bonds generated for 'chain 'C' and resid 255 through 258' Processing helix chain 'C' and resid 261 through 274 removed outlier: 3.774A pdb=" N PHE C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 313 through 323 removed outlier: 3.970A pdb=" N LEU C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ARG C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 352 through 360 removed outlier: 3.645A pdb=" N SER C 359 " --> pdb=" O THR C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 399 through 418 removed outlier: 3.698A pdb=" N ALA C 404 " --> pdb=" O LYS C 400 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU C 411 " --> pdb=" O MET C 407 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS C 414 " --> pdb=" O GLY C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 440 removed outlier: 3.801A pdb=" N ALA C 434 " --> pdb=" O MET C 430 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 439 " --> pdb=" O ARG C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.681A pdb=" N VAL C 458 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 503 through 509 removed outlier: 3.960A pdb=" N TYR C 508 " --> pdb=" O TYR C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 541 Proline residue: C 518 - end of helix removed outlier: 4.394A pdb=" N GLN C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG C 538 " --> pdb=" O ASN C 534 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN C 540 " --> pdb=" O GLN C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.568A pdb=" N LEU C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG C 560 " --> pdb=" O TYR C 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 190 through 205 removed outlier: 3.920A pdb=" N ALA A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 237 Processing helix chain 'A' and resid 255 through 274 removed outlier: 3.640A pdb=" N LEU A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 3.760A pdb=" N PHE A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.780A pdb=" N VAL A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.726A pdb=" N LEU A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 396 through 415 removed outlier: 4.088A pdb=" N VAL A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.595A pdb=" N ALA A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.787A pdb=" N VAL A 453 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 469 through 479 removed outlier: 4.029A pdb=" N LYS A 472 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 473 " --> pdb=" O TYR A 470 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 479 " --> pdb=" O PHE A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 501 through 509 removed outlier: 3.557A pdb=" N TYR A 504 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG A 507 " --> pdb=" O TYR A 504 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 509 " --> pdb=" O ILE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 534 Proline residue: A 518 - end of helix Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 545 through 561 removed outlier: 3.663A pdb=" N LEU A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 151 through 153 No H-bonds generated for 'chain 'B' and resid 151 through 153' Processing helix chain 'B' and resid 166 through 170 Processing helix chain 'B' and resid 192 through 199 Processing helix chain 'B' and resid 202 through 205 No H-bonds generated for 'chain 'B' and resid 202 through 205' Processing helix chain 'B' and resid 225 through 237 Processing helix chain 'B' and resid 255 through 258 No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 261 through 274 removed outlier: 3.668A pdb=" N GLU B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.561A pdb=" N TYR B 293 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 299 " --> pdb=" O GLN B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 313 through 323 removed outlier: 4.280A pdb=" N ARG B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 352 through 358 Processing helix chain 'B' and resid 369 through 372 No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 396 through 415 removed outlier: 4.231A pdb=" N LYS B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 440 removed outlier: 3.854A pdb=" N ALA B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 459 removed outlier: 3.741A pdb=" N VAL B 453 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 464 No H-bonds generated for 'chain 'B' and resid 462 through 464' Processing helix chain 'B' and resid 469 through 480 removed outlier: 4.286A pdb=" N LYS B 472 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 473 " --> pdb=" O TYR B 470 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 474 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 477 " --> pdb=" O TYR B 474 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 479 " --> pdb=" O PHE B 476 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B 480 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 487 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 517 through 534 removed outlier: 5.460A pdb=" N ILE B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 539 No H-bonds generated for 'chain 'B' and resid 536 through 539' Processing helix chain 'B' and resid 545 through 561 removed outlier: 3.529A pdb=" N GLN B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 154 No H-bonds generated for 'chain 'F' and resid 151 through 154' Processing helix chain 'F' and resid 173 through 187 removed outlier: 3.814A pdb=" N MET F 178 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS F 186 " --> pdb=" O ASN F 182 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 213 removed outlier: 3.678A pdb=" N THR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 240 Processing helix chain 'F' and resid 243 through 255 removed outlier: 3.876A pdb=" N TYR F 252 " --> pdb=" O THR F 248 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE F 253 " --> pdb=" O MET F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 282 removed outlier: 3.573A pdb=" N ASN F 275 " --> pdb=" O PHE F 271 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL F 278 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA F 280 " --> pdb=" O SER F 276 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 303 Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 330 through 335 removed outlier: 3.626A pdb=" N THR F 335 " --> pdb=" O ALA F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 351 Processing helix chain 'F' and resid 375 through 398 removed outlier: 3.849A pdb=" N GLU F 393 " --> pdb=" O THR F 389 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE F 397 " --> pdb=" O GLU F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 405 No H-bonds generated for 'chain 'F' and resid 403 through 405' Processing helix chain 'F' and resid 408 through 423 removed outlier: 3.606A pdb=" N ILE F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 435 removed outlier: 4.105A pdb=" N VAL F 433 " --> pdb=" O VAL F 430 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR F 435 " --> pdb=" O GLU F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 447 No H-bonds generated for 'chain 'F' and resid 445 through 447' Processing helix chain 'F' and resid 451 through 456 Processing helix chain 'F' and resid 473 through 500 removed outlier: 3.511A pdb=" N LYS F 482 " --> pdb=" O GLU F 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 52 No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 149 through 154 Processing helix chain 'D' and resid 173 through 184 removed outlier: 3.682A pdb=" N ILE D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 213 removed outlier: 3.559A pdb=" N THR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 255 removed outlier: 4.380A pdb=" N ARG D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE D 253 " --> pdb=" O MET D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 281 Processing helix chain 'D' and resid 295 through 303 removed outlier: 3.564A pdb=" N LEU D 302 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 330 through 338 removed outlier: 4.145A pdb=" N HIS D 338 " --> pdb=" O THR D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 375 through 398 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 408 through 423 removed outlier: 3.666A pdb=" N LYS D 422 " --> pdb=" O ARG D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 435 No H-bonds generated for 'chain 'D' and resid 432 through 435' Processing helix chain 'D' and resid 444 through 456 Processing helix chain 'D' and resid 465 through 467 No H-bonds generated for 'chain 'D' and resid 465 through 467' Processing helix chain 'D' and resid 473 through 500 removed outlier: 3.931A pdb=" N LYS D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS D 479 " --> pdb=" O SER D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 101 No H-bonds generated for 'chain 'E' and resid 99 through 101' Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 173 through 184 Processing helix chain 'E' and resid 201 through 213 Processing helix chain 'E' and resid 236 through 239 No H-bonds generated for 'chain 'E' and resid 236 through 239' Processing helix chain 'E' and resid 242 through 255 removed outlier: 3.828A pdb=" N PHE E 253 " --> pdb=" O MET E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 279 Processing helix chain 'E' and resid 295 through 303 removed outlier: 3.747A pdb=" N LEU E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 325 No H-bonds generated for 'chain 'E' and resid 323 through 325' Processing helix chain 'E' and resid 330 through 335 Processing helix chain 'E' and resid 348 through 352 Processing helix chain 'E' and resid 375 through 398 removed outlier: 3.624A pdb=" N ASP E 383 " --> pdb=" O ASN E 379 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP E 396 " --> pdb=" O LYS E 392 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE E 397 " --> pdb=" O GLU E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 405 No H-bonds generated for 'chain 'E' and resid 403 through 405' Processing helix chain 'E' and resid 408 through 423 removed outlier: 3.624A pdb=" N LYS E 419 " --> pdb=" O ASP E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 435 removed outlier: 4.230A pdb=" N VAL E 433 " --> pdb=" O VAL E 430 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR E 435 " --> pdb=" O GLU E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 455 Processing helix chain 'E' and resid 465 through 467 No H-bonds generated for 'chain 'E' and resid 465 through 467' Processing helix chain 'E' and resid 473 through 500 Processing helix chain 'L' and resid 40 through 47 Processing helix chain 'L' and resid 56 through 65 removed outlier: 3.935A pdb=" N VAL L 60 " --> pdb=" O GLY L 56 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 83 Processing helix chain 'L' and resid 97 through 109 Processing helix chain 'L' and resid 118 through 131 removed outlier: 4.141A pdb=" N TYR L 123 " --> pdb=" O GLU L 119 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL L 124 " --> pdb=" O SER L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 147 Processing helix chain 'L' and resid 153 through 168 removed outlier: 3.548A pdb=" N ALA L 158 " --> pdb=" O ALA L 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 48 Processing helix chain 'J' and resid 52 through 63 removed outlier: 4.011A pdb=" N GLY J 56 " --> pdb=" O TYR J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 83 Processing helix chain 'J' and resid 97 through 109 removed outlier: 3.885A pdb=" N ILE J 104 " --> pdb=" O ALA J 100 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU J 105 " --> pdb=" O MET J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 130 removed outlier: 3.512A pdb=" N VAL J 124 " --> pdb=" O SER J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 147 removed outlier: 3.545A pdb=" N VAL J 139 " --> pdb=" O ARG J 135 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU J 147 " --> pdb=" O GLY J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 168 removed outlier: 3.866A pdb=" N ALA J 158 " --> pdb=" O ALA J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 178 No H-bonds generated for 'chain 'J' and resid 175 through 178' Processing helix chain 'K' and resid 40 through 47 removed outlier: 3.521A pdb=" N GLU K 45 " --> pdb=" O PRO K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 64 Processing helix chain 'K' and resid 71 through 83 Processing helix chain 'K' and resid 97 through 109 removed outlier: 3.871A pdb=" N MET K 101 " --> pdb=" O LYS K 97 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU K 105 " --> pdb=" O MET K 101 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU K 106 " --> pdb=" O MET K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 131 removed outlier: 3.524A pdb=" N LYS K 126 " --> pdb=" O GLY K 122 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU K 127 " --> pdb=" O TYR K 123 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU K 128 " --> pdb=" O VAL K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 147 Processing helix chain 'K' and resid 153 through 168 removed outlier: 3.627A pdb=" N ALA K 158 " --> pdb=" O ALA K 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 32 Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.845A pdb=" N ALA M 53 " --> pdb=" O HIS M 49 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU M 56 " --> pdb=" O PHE M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 84 removed outlier: 3.602A pdb=" N PHE M 75 " --> pdb=" O VAL M 72 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP M 79 " --> pdb=" O LYS M 76 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE M 82 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 105 through 117 Processing helix chain 'M' and resid 120 through 122 No H-bonds generated for 'chain 'M' and resid 120 through 122' Processing helix chain 'M' and resid 124 through 137 removed outlier: 3.886A pdb=" N ALA M 129 " --> pdb=" O ASN M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 158 Processing helix chain 'M' and resid 160 through 169 removed outlier: 3.654A pdb=" N GLU M 165 " --> pdb=" O LYS M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 221 removed outlier: 3.541A pdb=" N ALA M 209 " --> pdb=" O ALA M 205 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR M 211 " --> pdb=" O ALA M 207 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA M 219 " --> pdb=" O ALA M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 245 Processing helix chain 'M' and resid 249 through 262 Processing helix chain 'G' and resid 4 through 43 removed outlier: 3.793A pdb=" N ARG G 8 " --> pdb=" O GLY G 4 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN G 22 " --> pdb=" O LYS G 18 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL G 40 " --> pdb=" O ARG G 36 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG G 41 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG G 43 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 56 No H-bonds generated for 'chain 'G' and resid 53 through 56' Processing helix chain 'G' and resid 63 through 69 removed outlier: 3.579A pdb=" N ILE G 67 " --> pdb=" O ASP G 63 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 98 removed outlier: 3.517A pdb=" N LEU G 96 " --> pdb=" O MET G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 120 removed outlier: 3.576A pdb=" N MET G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 151 removed outlier: 4.098A pdb=" N THR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 192 removed outlier: 3.737A pdb=" N ALA G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 214 Processing helix chain 'G' and resid 217 through 246 Processing helix chain 'G' and resid 249 through 294 removed outlier: 4.380A pdb=" N GLN G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY G 260 " --> pdb=" O GLY G 256 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS G 274 " --> pdb=" O ASN G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 30 Processing helix chain 'H' and resid 131 through 133 No H-bonds generated for 'chain 'H' and resid 131 through 133' Processing helix chain 'H' and resid 136 through 151 removed outlier: 3.739A pdb=" N LYS H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA H 142 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 175 removed outlier: 3.992A pdb=" N ILE H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN H 160 " --> pdb=" O ALA H 156 " (cutoff:3.500A) Proline residue: H 170 - end of helix Processing helix chain 'I' and resid 10 through 24 removed outlier: 3.871A pdb=" N GLU I 23 " --> pdb=" O ARG I 19 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL I 24 " --> pdb=" O CYS I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 37 removed outlier: 5.056A pdb=" N ARG I 36 " --> pdb=" O THR I 32 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 33 through 35 No H-bonds generated for 'chain 'O' and resid 33 through 35' Processing helix chain 'O' and resid 37 through 45 removed outlier: 3.897A pdb=" N GLY O 45 " --> pdb=" O MET O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 66 removed outlier: 3.861A pdb=" N GLY O 52 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 100 Proline residue: O 76 - end of helix removed outlier: 3.707A pdb=" N PHE O 82 " --> pdb=" O CYS O 78 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU O 88 " --> pdb=" O LEU O 84 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA O 96 " --> pdb=" O THR O 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 35 No H-bonds generated for 'chain 'P' and resid 33 through 35' Processing helix chain 'P' and resid 37 through 46 removed outlier: 3.581A pdb=" N SER P 44 " --> pdb=" O GLY P 40 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY P 45 " --> pdb=" O MET P 41 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL P 46 " --> pdb=" O ALA P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 66 removed outlier: 3.910A pdb=" N GLY P 52 " --> pdb=" O VAL P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 98 removed outlier: 4.143A pdb=" N ALA P 72 " --> pdb=" O ASN P 69 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS P 73 " --> pdb=" O MET P 70 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU P 74 " --> pdb=" O SER P 71 " (cutoff:3.500A) Proline residue: P 76 - end of helix removed outlier: 3.764A pdb=" N LEU P 80 " --> pdb=" O TYR P 77 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE P 82 " --> pdb=" O ILE P 79 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA P 87 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU P 88 " --> pdb=" O SER P 85 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE P 95 " --> pdb=" O THR P 92 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU P 98 " --> pdb=" O ILE P 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 45 removed outlier: 3.901A pdb=" N ILE Q 37 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY Q 38 " --> pdb=" O ASN Q 35 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA Q 39 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA Q 42 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 66 removed outlier: 4.243A pdb=" N ALA Q 54 " --> pdb=" O ILE Q 51 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER Q 58 " --> pdb=" O MET Q 55 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER Q 59 " --> pdb=" O CYS Q 56 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA Q 63 " --> pdb=" O TYR Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 70 No H-bonds generated for 'chain 'Q' and resid 68 through 70' Processing helix chain 'Q' and resid 75 through 101 removed outlier: 3.828A pdb=" N PHE Q 82 " --> pdb=" O CYS Q 78 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER Q 85 " --> pdb=" O GLY Q 81 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA Q 89 " --> pdb=" O SER Q 85 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 46 removed outlier: 3.763A pdb=" N ILE R 37 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLY R 38 " --> pdb=" O ASN R 35 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA R 39 " --> pdb=" O LEU R 36 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA R 43 " --> pdb=" O GLY R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 66 Processing helix chain 'R' and resid 69 through 98 removed outlier: 4.091A pdb=" N ALA R 72 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU R 74 " --> pdb=" O SER R 71 " (cutoff:3.500A) Proline residue: R 76 - end of helix removed outlier: 3.581A pdb=" N ILE R 79 " --> pdb=" O PRO R 76 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU R 84 " --> pdb=" O GLY R 81 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU R 88 " --> pdb=" O SER R 85 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA R 96 " --> pdb=" O LEU R 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 35 No H-bonds generated for 'chain 'S' and resid 33 through 35' Processing helix chain 'S' and resid 37 through 45 removed outlier: 3.957A pdb=" N SER S 44 " --> pdb=" O GLY S 40 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY S 45 " --> pdb=" O MET S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 66 removed outlier: 3.537A pdb=" N CYS S 56 " --> pdb=" O GLY S 52 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE S 57 " --> pdb=" O VAL S 53 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU S 62 " --> pdb=" O SER S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 74 removed outlier: 4.410A pdb=" N ALA S 72 " --> pdb=" O ASN S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 98 removed outlier: 3.762A pdb=" N LEU S 80 " --> pdb=" O PRO S 76 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY S 81 " --> pdb=" O TYR S 77 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU S 88 " --> pdb=" O LEU S 84 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA S 89 " --> pdb=" O SER S 85 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE S 95 " --> pdb=" O PHE S 91 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA S 96 " --> pdb=" O THR S 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 35 Processing helix chain 'T' and resid 37 through 45 removed outlier: 3.878A pdb=" N MET T 41 " --> pdb=" O ILE T 37 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY T 45 " --> pdb=" O MET T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 66 removed outlier: 4.331A pdb=" N ALA T 54 " --> pdb=" O ILE T 51 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET T 55 " --> pdb=" O GLY T 52 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER T 58 " --> pdb=" O MET T 55 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER T 59 " --> pdb=" O CYS T 56 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU T 62 " --> pdb=" O SER T 59 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA T 64 " --> pdb=" O MET T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 68 through 98 removed outlier: 4.354A pdb=" N ALA T 72 " --> pdb=" O ASN T 69 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU T 74 " --> pdb=" O SER T 71 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU T 75 " --> pdb=" O ALA T 72 " (cutoff:3.500A) Proline residue: T 76 - end of helix removed outlier: 3.601A pdb=" N GLY T 81 " --> pdb=" O CYS T 78 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU T 84 " --> pdb=" O GLY T 81 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA T 87 " --> pdb=" O LEU T 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 35 No H-bonds generated for 'chain 'U' and resid 33 through 35' Processing helix chain 'U' and resid 38 through 45 removed outlier: 4.112A pdb=" N GLY U 45 " --> pdb=" O MET U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 66 removed outlier: 3.629A pdb=" N TYR U 60 " --> pdb=" O CYS U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 98 removed outlier: 4.208A pdb=" N ALA U 72 " --> pdb=" O ASN U 69 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU U 74 " --> pdb=" O SER U 71 " (cutoff:3.500A) Proline residue: U 76 - end of helix removed outlier: 3.838A pdb=" N ILE U 79 " --> pdb=" O PRO U 76 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU U 80 " --> pdb=" O TYR U 77 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA U 83 " --> pdb=" O LEU U 80 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU U 84 " --> pdb=" O GLY U 81 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE U 95 " --> pdb=" O THR U 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 45 removed outlier: 3.810A pdb=" N ILE V 37 " --> pdb=" O ALA V 34 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLY V 38 " --> pdb=" O ASN V 35 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA V 42 " --> pdb=" O ALA V 39 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA V 43 " --> pdb=" O GLY V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 66 removed outlier: 3.522A pdb=" N SER V 59 " --> pdb=" O MET V 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 98 removed outlier: 4.226A pdb=" N ALA V 72 " --> pdb=" O ASN V 69 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU V 74 " --> pdb=" O SER V 71 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU V 75 " --> pdb=" O ALA V 72 " (cutoff:3.500A) Proline residue: V 76 - end of helix removed outlier: 4.189A pdb=" N ILE V 79 " --> pdb=" O PRO V 76 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU V 80 " --> pdb=" O TYR V 77 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU V 84 " --> pdb=" O GLY V 81 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA V 87 " --> pdb=" O LEU V 84 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE V 95 " --> pdb=" O THR V 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 35 No H-bonds generated for 'chain 'W' and resid 33 through 35' Processing helix chain 'W' and resid 37 through 46 removed outlier: 4.280A pdb=" N MET W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL W 46 " --> pdb=" O ALA W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 66 removed outlier: 3.771A pdb=" N MET W 55 " --> pdb=" O GLY W 52 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER W 58 " --> pdb=" O MET W 55 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER W 59 " --> pdb=" O CYS W 56 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA W 63 " --> pdb=" O TYR W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 101 removed outlier: 4.686A pdb=" N ALA W 72 " --> pdb=" O ASN W 69 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU W 75 " --> pdb=" O ALA W 72 " (cutoff:3.500A) Proline residue: W 76 - end of helix removed outlier: 3.849A pdb=" N ILE W 79 " --> pdb=" O PRO W 76 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU W 80 " --> pdb=" O TYR W 77 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY W 81 " --> pdb=" O CYS W 78 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE W 82 " --> pdb=" O ILE W 79 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU W 84 " --> pdb=" O GLY W 81 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU W 88 " --> pdb=" O SER W 85 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU W 90 " --> pdb=" O ALA W 87 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR W 92 " --> pdb=" O ALA W 89 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE W 95 " --> pdb=" O THR W 92 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA W 96 " --> pdb=" O LEU W 93 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU W 100 " --> pdb=" O LEU W 97 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE W 101 " --> pdb=" O LEU W 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 46 removed outlier: 3.885A pdb=" N ILE X 37 " --> pdb=" O ALA X 34 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY X 38 " --> pdb=" O ASN X 35 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY X 40 " --> pdb=" O ILE X 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET X 41 " --> pdb=" O GLY X 38 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY X 45 " --> pdb=" O ALA X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 66 removed outlier: 3.534A pdb=" N PHE X 57 " --> pdb=" O ALA X 54 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG X 66 " --> pdb=" O ALA X 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 68 through 70 No H-bonds generated for 'chain 'X' and resid 68 through 70' Processing helix chain 'X' and resid 75 through 100 removed outlier: 3.861A pdb=" N GLY X 81 " --> pdb=" O TYR X 77 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE X 82 " --> pdb=" O CYS X 78 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU X 88 " --> pdb=" O LEU X 84 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA X 96 " --> pdb=" O THR X 92 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU X 100 " --> pdb=" O ALA X 96 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.770A pdb=" N GLY C 81 " --> pdb=" O PHE C 72 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 105 through 107 Processing sheet with id= C, first strand: chain 'C' and resid 245 through 249 removed outlier: 3.519A pdb=" N LEU C 215 " --> pdb=" O HIS C 278 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N SER C 335 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU C 281 " --> pdb=" O SER C 335 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR C 337 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR C 283 " --> pdb=" O THR C 337 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU C 339 " --> pdb=" O TYR C 283 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 30 through 36 removed outlier: 6.767A pdb=" N THR C 41 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 39 " --> pdb=" O ILE C 35 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.721A pdb=" N THR A 41 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN A 73 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE A 83 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL A 71 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 57 through 59 Processing sheet with id= G, first strand: chain 'A' and resid 105 through 107 Processing sheet with id= H, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.464A pdb=" N ILE A 246 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR A 218 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA A 249 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N SER A 220 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A 282 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE A 221 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASP A 284 " --> pdb=" O ILE A 221 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.950A pdb=" N GLY B 30 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA B 99 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS B 28 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR B 41 " --> pdb=" O HIS B 33 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 80 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 83 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL B 71 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.499A pdb=" N ILE B 246 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 21 through 26 removed outlier: 3.509A pdb=" N TYR F 21 " --> pdb=" O THR F 33 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP F 31 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE F 25 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL F 29 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN F 62 " --> pdb=" O ARG F 70 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE F 72 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE F 60 " --> pdb=" O ILE F 72 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 163 through 166 removed outlier: 6.689A pdb=" N ALA F 341 " --> pdb=" O GLY F 164 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N PHE F 166 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR F 343 " --> pdb=" O PHE F 166 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'F' and resid 226 through 230 removed outlier: 8.105A pdb=" N VAL F 193 " --> pdb=" O ASP F 260 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU F 262 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ALA F 195 " --> pdb=" O LEU F 262 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE F 264 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL F 197 " --> pdb=" O PHE F 264 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP F 266 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER F 313 " --> pdb=" O VAL F 261 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU F 263 " --> pdb=" O SER F 313 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR F 315 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL F 265 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL F 317 " --> pdb=" O VAL F 265 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 85 through 87 removed outlier: 6.829A pdb=" N ASP D 31 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE D 25 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL D 29 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE D 72 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE D 60 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 56 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 94 through 96 Processing sheet with id= P, first strand: chain 'D' and resid 316 through 319 removed outlier: 6.508A pdb=" N ALA D 341 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N PHE D 166 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR D 343 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 262 through 265 Processing sheet with id= R, first strand: chain 'E' and resid 19 through 21 Processing sheet with id= S, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.589A pdb=" N GLN E 62 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE E 72 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE E 60 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 56 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 94 through 96 Processing sheet with id= U, first strand: chain 'E' and resid 342 through 344 removed outlier: 8.352A pdb=" N THR E 343 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY E 164 " --> pdb=" O THR E 343 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE E 163 " --> pdb=" O ILE E 314 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER E 316 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU E 165 " --> pdb=" O SER E 316 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLN E 318 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E 261 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL E 317 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU E 263 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA E 319 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL E 265 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'M' and resid 140 through 146 removed outlier: 5.694A pdb=" N LYS M 176 " --> pdb=" O THR M 141 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ALA M 143 " --> pdb=" O LYS M 176 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL M 178 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL M 145 " --> pdb=" O VAL M 178 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU M 180 " --> pdb=" O VAL M 145 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'M' and resid 190 through 194 Processing sheet with id= X, first strand: chain 'G' and resid 74 through 77 removed outlier: 6.322A pdb=" N SER G 169 " --> pdb=" O HIS G 165 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 106 through 109 removed outlier: 7.701A pdb=" N SER G 108 " --> pdb=" O ARG G 126 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR G 128 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 85 through 88 removed outlier: 7.200A pdb=" N LEU H 51 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS H 60 " --> pdb=" O LEU H 51 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 75 through 78 removed outlier: 4.231A pdb=" N ARG H 70 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE H 93 " --> pdb=" O ARG H 70 " (cutoff:3.500A) 1505 hydrogen bonds defined for protein. 3867 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: 29.04 Time building geometry restraints manager: 58.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 39771 1.02 - 1.22: 66 1.22 - 1.42: 16072 1.42 - 1.62: 23546 1.62 - 1.82: 402 Bond restraints: 79857 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.18e+01 bond pdb=" C4 ATP E 601 " pdb=" C5 ATP E 601 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.46e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.45e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.38e+01 bond pdb=" C5 ATP C 601 " pdb=" C6 ATP C 601 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.27e+01 ... (remaining 79852 not shown) Histogram of bond angle deviations from ideal: 97.72 - 105.44: 888 105.44 - 113.15: 96396 113.15 - 120.87: 29849 120.87 - 128.59: 17389 128.59 - 136.30: 268 Bond angle restraints: 144790 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 115.96 23.91 1.00e+00 1.00e+00 5.72e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 117.31 22.56 1.00e+00 1.00e+00 5.09e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 117.57 22.30 1.00e+00 1.00e+00 4.97e+02 angle pdb=" PB ATP E 601 " pdb=" O3B ATP E 601 " pdb=" PG ATP E 601 " ideal model delta sigma weight residual 139.87 118.09 21.78 1.00e+00 1.00e+00 4.74e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 118.93 17.90 1.00e+00 1.00e+00 3.20e+02 ... (remaining 144785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 29562 17.78 - 35.56: 1885 35.56 - 53.35: 191 53.35 - 71.13: 22 71.13 - 88.91: 8 Dihedral angle restraints: 31668 sinusoidal: 14849 harmonic: 16819 Sorted by residual: dihedral pdb=" CA ILE A 117 " pdb=" C ILE A 117 " pdb=" N ASN A 118 " pdb=" CA ASN A 118 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ALA D 287 " pdb=" C ALA D 287 " pdb=" N ALA D 288 " pdb=" CA ALA D 288 " ideal model delta harmonic sigma weight residual 180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ASP B 284 " pdb=" C ASP B 284 " pdb=" N ASP B 285 " pdb=" CA ASP B 285 " ideal model delta harmonic sigma weight residual 180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 31665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 6030 0.098 - 0.197: 275 0.197 - 0.295: 2 0.295 - 0.394: 0 0.394 - 0.492: 1 Chirality restraints: 6308 Sorted by residual: chirality pdb=" CG LEU F 82 " pdb=" CB LEU F 82 " pdb=" CD1 LEU F 82 " pdb=" CD2 LEU F 82 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" CA ARG F 83 " pdb=" N ARG F 83 " pdb=" C ARG F 83 " pdb=" CB ARG F 83 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ILE M 146 " pdb=" N ILE M 146 " pdb=" C ILE M 146 " pdb=" CB ILE M 146 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 6305 not shown) Planarity restraints: 11833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 385 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C VAL F 385 " 0.072 2.00e-02 2.50e+03 pdb=" O VAL F 385 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU F 386 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 318 " -0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C SER A 318 " 0.069 2.00e-02 2.50e+03 pdb=" O SER A 318 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG A 319 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 315 " -0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C TYR A 315 " 0.068 2.00e-02 2.50e+03 pdb=" O TYR A 315 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU A 316 " -0.023 2.00e-02 2.50e+03 ... (remaining 11830 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.07: 865 2.07 - 2.70: 134124 2.70 - 3.33: 232307 3.33 - 3.97: 294729 3.97 - 4.60: 477605 Nonbonded interactions: 1139630 Sorted by model distance: nonbonded pdb=" PB ATP A 601 " pdb="MG MG A 602 " model vdw 1.432 2.450 nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 1.443 2.050 nonbonded pdb="HG21 THR F 174 " pdb="MG MG F 602 " model vdw 1.496 1.870 nonbonded pdb=" O ASP F 450 " pdb=" HG SER F 453 " model vdw 1.636 1.850 nonbonded pdb=" O ALA T 54 " pdb=" H SER T 58 " model vdw 1.652 1.850 ... (remaining 1139625 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 'B' and ((resid 26 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 27 through 562 or resid 601 through 602)) selection = (chain 'C' and ((resid 26 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 27 through 562 or resid 601 through 602)) } ncs_group { reference = (chain 'D' and (resid 15 through 173 or (resid 174 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 175 through 501)) selection = (chain 'E' and resid 15 through 501) selection = (chain 'F' and (resid 15 through 173 or (resid 174 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 175 through 501)) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 14 5.49 5 Mg 5 5.21 5 S 233 5.16 5 C 25085 2.51 5 N 6559 2.21 5 O 7457 1.98 5 H 39835 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: 4.320 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: 0.930 Extract box with map and model: 23.170 Check model and map are aligned: 0.960 Convert atoms to be neutral: 0.520 Process input model: 198.670 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 234.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.007 0.086 40022 Z= 0.474 Angle : 0.810 23.911 54248 Z= 0.492 Chirality : 0.046 0.492 6308 Planarity : 0.006 0.070 6928 Dihedral : 11.469 88.912 14685 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.03 % Favored : 95.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -3.76 (0.10), residues: 5084 helix: -2.58 (0.07), residues: 2437 sheet: -3.22 (0.17), residues: 572 loop : -1.89 (0.13), residues: 2075 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 904 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 904 time to evaluate : 4.904 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 904 average time/residue: 1.0374 time to fit residues: 1495.9313 Evaluate side-chains 526 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 526 time to evaluate : 4.862 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 428 optimal weight: 9.9990 chunk 384 optimal weight: 6.9990 chunk 213 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 259 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 397 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 295 optimal weight: 4.9990 chunk 460 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN C 395 ASN ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN B 441 ASN B 469 GLN B 550 GLN F 18 GLN F 188 HIS D 62 GLN D 115 GLN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 ASN ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 40022 Z= 0.258 Angle : 0.569 6.627 54248 Z= 0.301 Chirality : 0.040 0.160 6308 Planarity : 0.004 0.056 6928 Dihedral : 4.972 70.078 5560 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.60 % Favored : 96.38 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.11), residues: 5084 helix: -1.03 (0.10), residues: 2481 sheet: -2.78 (0.18), residues: 591 loop : -1.39 (0.14), residues: 2012 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 621 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 563 time to evaluate : 4.921 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 outliers start: 58 outliers final: 42 residues processed: 601 average time/residue: 0.9619 time to fit residues: 944.0970 Evaluate side-chains 525 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 483 time to evaluate : 4.865 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.6845 time to fit residues: 59.3364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 255 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 383 optimal weight: 7.9990 chunk 313 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 461 optimal weight: 5.9990 chunk 498 optimal weight: 9.9990 chunk 410 optimal weight: 3.9990 chunk 457 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 370 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 GLN B 501 ASN B 534 ASN D 231 GLN D 233 ASN D 275 ASN ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.063 40022 Z= 0.440 Angle : 0.647 10.057 54248 Z= 0.346 Chirality : 0.043 0.180 6308 Planarity : 0.005 0.074 6928 Dihedral : 5.202 76.135 5560 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.78 % Favored : 94.20 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -1.92 (0.11), residues: 5084 helix: -0.62 (0.10), residues: 2497 sheet: -2.75 (0.19), residues: 597 loop : -1.44 (0.14), residues: 1990 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 542 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 497 time to evaluate : 4.873 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 outliers start: 45 outliers final: 35 residues processed: 523 average time/residue: 0.9828 time to fit residues: 843.3962 Evaluate side-chains 491 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 456 time to evaluate : 4.988 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.7372 time to fit residues: 54.3250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 455 optimal weight: 10.0000 chunk 346 optimal weight: 0.9990 chunk 239 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 309 optimal weight: 4.9990 chunk 462 optimal weight: 0.7980 chunk 490 optimal weight: 0.9990 chunk 241 optimal weight: 3.9990 chunk 438 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 40022 Z= 0.180 Angle : 0.513 6.726 54248 Z= 0.265 Chirality : 0.039 0.149 6308 Planarity : 0.004 0.053 6928 Dihedral : 4.820 73.802 5560 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -1.34 (0.12), residues: 5084 helix: -0.19 (0.10), residues: 2503 sheet: -2.53 (0.20), residues: 583 loop : -1.08 (0.14), residues: 1998 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 510 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 492 time to evaluate : 4.962 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: 18 outliers final: 13 residues processed: 502 average time/residue: 0.9625 time to fit residues: 790.4937 Evaluate side-chains 477 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 464 time to evaluate : 4.922 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.8128 time to fit residues: 24.4330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 408 optimal weight: 6.9990 chunk 278 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 364 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 418 optimal weight: 8.9990 chunk 338 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 439 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 40022 Z= 0.331 Angle : 0.566 6.772 54248 Z= 0.297 Chirality : 0.041 0.168 6308 Planarity : 0.004 0.080 6928 Dihedral : 4.932 74.970 5560 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.66 % Favored : 94.30 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -1.30 (0.12), residues: 5084 helix: -0.12 (0.10), residues: 2532 sheet: -2.53 (0.19), residues: 594 loop : -1.11 (0.14), residues: 1958 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 510 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 475 time to evaluate : 4.929 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 outliers start: 35 outliers final: 25 residues processed: 498 average time/residue: 1.0178 time to fit residues: 836.4652 Evaluate side-chains 482 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 457 time to evaluate : 4.851 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.7641 time to fit residues: 41.0188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 164 optimal weight: 0.7980 chunk 441 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 490 optimal weight: 5.9990 chunk 407 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 257 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 ASN ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 40022 Z= 0.220 Angle : 0.509 6.442 54248 Z= 0.264 Chirality : 0.039 0.151 6308 Planarity : 0.004 0.060 6928 Dihedral : 4.726 74.982 5560 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.76 % Favored : 96.22 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -0.95 (0.12), residues: 5084 helix: 0.15 (0.11), residues: 2516 sheet: -2.36 (0.20), residues: 591 loop : -0.90 (0.15), residues: 1977 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 502 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 479 time to evaluate : 4.999 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: 23 outliers final: 12 residues processed: 488 average time/residue: 1.0082 time to fit residues: 812.5988 Evaluate side-chains 466 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 454 time to evaluate : 4.886 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.7743 time to fit residues: 22.3815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 472 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 358 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 412 optimal weight: 8.9990 chunk 273 optimal weight: 2.9990 chunk 488 optimal weight: 9.9990 chunk 305 optimal weight: 3.9990 chunk 297 optimal weight: 5.9990 chunk 225 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 HIS ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 40022 Z= 0.321 Angle : 0.552 6.608 54248 Z= 0.290 Chirality : 0.040 0.168 6308 Planarity : 0.004 0.077 6928 Dihedral : 4.841 76.340 5560 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.74 % Favored : 94.22 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -1.02 (0.12), residues: 5084 helix: 0.10 (0.10), residues: 2541 sheet: -2.42 (0.20), residues: 595 loop : -0.97 (0.14), residues: 1948 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 480 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 462 time to evaluate : 5.107 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 outliers start: 18 outliers final: 14 residues processed: 475 average time/residue: 1.0100 time to fit residues: 790.3616 Evaluate side-chains 460 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 446 time to evaluate : 4.945 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.7872 time to fit residues: 26.1602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 302 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 291 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 310 optimal weight: 0.0030 chunk 332 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 384 optimal weight: 4.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 40022 Z= 0.319 Angle : 0.555 7.109 54248 Z= 0.292 Chirality : 0.041 0.166 6308 Planarity : 0.004 0.069 6928 Dihedral : 4.906 77.275 5560 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.74 % Favored : 94.24 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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 (0.12), residues: 5084 helix: 0.14 (0.10), residues: 2532 sheet: -2.39 (0.20), residues: 593 loop : -0.98 (0.14), residues: 1959 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 485 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 458 time to evaluate : 4.975 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 outliers start: 27 outliers final: 19 residues processed: 472 average time/residue: 0.9771 time to fit residues: 765.1150 Evaluate side-chains 466 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 447 time to evaluate : 4.874 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.7269 time to fit residues: 31.2123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 444 optimal weight: 20.0000 chunk 468 optimal weight: 9.9990 chunk 427 optimal weight: 8.9990 chunk 455 optimal weight: 9.9990 chunk 274 optimal weight: 0.7980 chunk 198 optimal weight: 5.9990 chunk 357 optimal weight: 0.9990 chunk 139 optimal weight: 0.0470 chunk 411 optimal weight: 1.9990 chunk 430 optimal weight: 9.9990 chunk 453 optimal weight: 8.9990 overall best weight: 1.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 HIS ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 40022 Z= 0.276 Angle : 0.541 8.107 54248 Z= 0.280 Chirality : 0.040 0.221 6308 Planarity : 0.004 0.067 6928 Dihedral : 4.865 78.105 5560 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.45 % Favored : 94.53 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -0.88 (0.12), residues: 5084 helix: 0.23 (0.11), residues: 2522 sheet: -2.32 (0.20), residues: 589 loop : -0.91 (0.14), residues: 1973 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 470 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 456 time to evaluate : 5.113 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 outliers start: 14 outliers final: 8 residues processed: 466 average time/residue: 0.9913 time to fit residues: 762.0363 Evaluate side-chains 452 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 444 time to evaluate : 4.840 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.7205 time to fit residues: 16.5174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 299 optimal weight: 5.9990 chunk 481 optimal weight: 10.0000 chunk 293 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 334 optimal weight: 2.9990 chunk 505 optimal weight: 9.9990 chunk 464 optimal weight: 0.9980 chunk 402 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 310 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 40022 Z= 0.259 Angle : 0.535 11.385 54248 Z= 0.277 Chirality : 0.040 0.158 6308 Planarity : 0.004 0.065 6928 Dihedral : 4.836 78.621 5560 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.21 % Favored : 94.77 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -0.80 (0.12), residues: 5084 helix: 0.29 (0.11), residues: 2518 sheet: -2.28 (0.20), residues: 589 loop : -0.87 (0.14), residues: 1977 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 465 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 458 time to evaluate : 5.052 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 outliers start: 7 outliers final: 5 residues processed: 460 average time/residue: 0.9690 time to fit residues: 738.0155 Evaluate side-chains 450 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 445 time to evaluate : 4.887 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.7516 time to fit residues: 12.7050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 319 optimal weight: 2.9990 chunk 428 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 chunk 370 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 402 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 413 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 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 = 0.3615 r_free = 0.3615 target = 0.093920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.067278 restraints weight = 327226.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.067761 restraints weight = 161475.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.067715 restraints weight = 110295.772| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 40022 Z= 0.251 Angle : 0.540 11.732 54248 Z= 0.277 Chirality : 0.040 0.157 6308 Planarity : 0.004 0.078 6928 Dihedral : 4.805 79.087 5560 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.33 % Favored : 94.65 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -0.75 (0.12), residues: 5084 helix: 0.33 (0.11), residues: 2527 sheet: -2.27 (0.20), residues: 589 loop : -0.85 (0.15), residues: 1968 =============================================================================== Job complete usr+sys time: 14234.81 seconds wall clock time: 248 minutes 1.65 seconds (14881.65 seconds total)