Starting phenix.real_space_refine (version: dev) on Mon Feb 27 15:27:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riq_4897/02_2023/6riq_4897_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riq_4897/02_2023/6riq_4897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riq_4897/02_2023/6riq_4897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riq_4897/02_2023/6riq_4897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riq_4897/02_2023/6riq_4897_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riq_4897/02_2023/6riq_4897_neut_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 Process input model Symmetric amino acids flipped Residue "A ASP 176": "OD1" <-> "OD2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A ARG 240": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 238": "OD1" <-> "OD2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B ARG 241": "NH1" <-> "NH2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C ASP 151": "OD1" <-> "OD2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C ARG 205": "NH1" <-> "NH2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "D ASP 151": "OD1" <-> "OD2" Residue "D GLU 167": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ASP 196": "OD1" <-> "OD2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D ASP 229": "OD1" <-> "OD2" Residue "D ASP 233": "OD1" <-> "OD2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E ARG 204": "NH1" <-> "NH2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 238": "OD1" <-> "OD2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "E ARG 241": "NH1" <-> "NH2" Residue "E ASP 256": "OD1" <-> "OD2" Residue "E ARG 262": "NH1" <-> "NH2" Residue "F ASP 176": "OD1" <-> "OD2" Residue "F ARG 202": "NH1" <-> "NH2" Residue "F ARG 204": "NH1" <-> "NH2" Residue "F ARG 216": "NH1" <-> "NH2" Residue "F PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 238": "OD1" <-> "OD2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "F ARG 241": "NH1" <-> "NH2" Residue "F ASP 256": "OD1" <-> "OD2" Residue "F ARG 262": "NH1" <-> "NH2" Residue "G ARG 30": "NH1" <-> "NH2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "G ARG 110": "NH1" <-> "NH2" Residue "G ASP 136": "OD1" <-> "OD2" Residue "G ASP 151": "OD1" <-> "OD2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G GLU 171": "OE1" <-> "OE2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ARG 205": "NH1" <-> "NH2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "G ASP 229": "OD1" <-> "OD2" Residue "G ASP 233": "OD1" <-> "OD2" Residue "H ASP 176": "OD1" <-> "OD2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "H GLU 225": "OE1" <-> "OE2" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 238": "OD1" <-> "OD2" Residue "H ARG 240": "NH1" <-> "NH2" Residue "H ARG 241": "NH1" <-> "NH2" Residue "H ASP 256": "OD1" <-> "OD2" Residue "H ARG 262": "NH1" <-> "NH2" Residue "I ASP 176": "OD1" <-> "OD2" Residue "I ARG 202": "NH1" <-> "NH2" Residue "I ARG 204": "NH1" <-> "NH2" Residue "I ARG 216": "NH1" <-> "NH2" Residue "I PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 225": "OE1" <-> "OE2" Residue "I TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 238": "OD1" <-> "OD2" Residue "I ARG 240": "NH1" <-> "NH2" Residue "I ARG 241": "NH1" <-> "NH2" Residue "I ASP 256": "OD1" <-> "OD2" Residue "I ARG 262": "NH1" <-> "NH2" Residue "J ARG 30": "NH1" <-> "NH2" Residue "J ASP 47": "OD1" <-> "OD2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J GLU 108": "OE1" <-> "OE2" Residue "J ARG 110": "NH1" <-> "NH2" Residue "J ASP 136": "OD1" <-> "OD2" Residue "J ASP 151": "OD1" <-> "OD2" Residue "J GLU 167": "OE1" <-> "OE2" Residue "J GLU 171": "OE1" <-> "OE2" Residue "J ASP 196": "OD1" <-> "OD2" Residue "J ARG 205": "NH1" <-> "NH2" Residue "J GLU 212": "OE1" <-> "OE2" Residue "J ASP 229": "OD1" <-> "OD2" Residue "J ASP 233": "OD1" <-> "OD2" Residue "K ARG 30": "NH1" <-> "NH2" Residue "K ASP 47": "OD1" <-> "OD2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K GLU 100": "OE1" <-> "OE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "K ARG 110": "NH1" <-> "NH2" Residue "K ASP 136": "OD1" <-> "OD2" Residue "K ASP 151": "OD1" <-> "OD2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K GLU 171": "OE1" <-> "OE2" Residue "K ASP 196": "OD1" <-> "OD2" Residue "K ARG 205": "NH1" <-> "NH2" Residue "K GLU 212": "OE1" <-> "OE2" Residue "K ASP 229": "OD1" <-> "OD2" Residue "K ASP 233": "OD1" <-> "OD2" Residue "L ASP 176": "OD1" <-> "OD2" Residue "L ARG 202": "NH1" <-> "NH2" Residue "L ARG 204": "NH1" <-> "NH2" Residue "L ARG 216": "NH1" <-> "NH2" Residue "L PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 225": "OE1" <-> "OE2" Residue "L TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 238": "OD1" <-> "OD2" Residue "L ARG 240": "NH1" <-> "NH2" Residue "L ARG 241": "NH1" <-> "NH2" Residue "L ASP 256": "OD1" <-> "OD2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "M ARG 30": "NH1" <-> "NH2" Residue "M ASP 47": "OD1" <-> "OD2" Residue "M GLU 100": "OE1" <-> "OE2" Residue "M GLU 108": "OE1" <-> "OE2" Residue "M ARG 110": "NH1" <-> "NH2" Residue "M ASP 136": "OD1" <-> "OD2" Residue "M ASP 151": "OD1" <-> "OD2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "M GLU 171": "OE1" <-> "OE2" Residue "M ASP 196": "OD1" <-> "OD2" Residue "M ARG 205": "NH1" <-> "NH2" Residue "M GLU 212": "OE1" <-> "OE2" Residue "M ASP 229": "OD1" <-> "OD2" Residue "M ASP 233": "OD1" <-> "OD2" Residue "N ARG 30": "NH1" <-> "NH2" Residue "N ASP 47": "OD1" <-> "OD2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N GLU 100": "OE1" <-> "OE2" Residue "N GLU 108": "OE1" <-> "OE2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "N ASP 136": "OD1" <-> "OD2" Residue "N ASP 151": "OD1" <-> "OD2" Residue "N GLU 167": "OE1" <-> "OE2" Residue "N GLU 171": "OE1" <-> "OE2" Residue "N ASP 196": "OD1" <-> "OD2" Residue "N ARG 205": "NH1" <-> "NH2" Residue "N GLU 212": "OE1" <-> "OE2" Residue "N ASP 229": "OD1" <-> "OD2" Residue "N ASP 233": "OD1" <-> "OD2" Residue "O ASP 176": "OD1" <-> "OD2" Residue "O ARG 202": "NH1" <-> "NH2" Residue "O ARG 204": "NH1" <-> "NH2" Residue "O ARG 216": "NH1" <-> "NH2" Residue "O GLU 225": "OE1" <-> "OE2" Residue "O TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 238": "OD1" <-> "OD2" Residue "O ARG 240": "NH1" <-> "NH2" Residue "O ARG 241": "NH1" <-> "NH2" Residue "O ASP 256": "OD1" <-> "OD2" Residue "O ARG 262": "NH1" <-> "NH2" Residue "P ASP 176": "OD1" <-> "OD2" Residue "P ARG 202": "NH1" <-> "NH2" Residue "P ARG 204": "NH1" <-> "NH2" Residue "P ARG 216": "NH1" <-> "NH2" Residue "P PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 225": "OE1" <-> "OE2" Residue "P TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 238": "OD1" <-> "OD2" Residue "P ARG 240": "NH1" <-> "NH2" Residue "P ARG 241": "NH1" <-> "NH2" Residue "P ASP 256": "OD1" <-> "OD2" Residue "P ARG 262": "NH1" <-> "NH2" Residue "Q ARG 30": "NH1" <-> "NH2" Residue "Q ASP 47": "OD1" <-> "OD2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 108": "OE1" <-> "OE2" Residue "Q ARG 110": "NH1" <-> "NH2" Residue "Q ASP 136": "OD1" <-> "OD2" Residue "Q ASP 151": "OD1" <-> "OD2" Residue "Q GLU 167": "OE1" <-> "OE2" Residue "Q GLU 171": "OE1" <-> "OE2" Residue "Q ASP 196": "OD1" <-> "OD2" Residue "Q ARG 205": "NH1" <-> "NH2" Residue "Q GLU 212": "OE1" <-> "OE2" Residue "Q ASP 229": "OD1" <-> "OD2" Residue "Q ASP 233": "OD1" <-> "OD2" Residue "R ARG 30": "NH1" <-> "NH2" Residue "R ASP 47": "OD1" <-> "OD2" Residue "R GLU 81": "OE1" <-> "OE2" Residue "R GLU 100": "OE1" <-> "OE2" Residue "R GLU 108": "OE1" <-> "OE2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "R ASP 136": "OD1" <-> "OD2" Residue "R ASP 151": "OD1" <-> "OD2" Residue "R GLU 167": "OE1" <-> "OE2" Residue "R GLU 171": "OE1" <-> "OE2" Residue "R ASP 196": "OD1" <-> "OD2" Residue "R ARG 205": "NH1" <-> "NH2" Residue "R GLU 212": "OE1" <-> "OE2" Residue "R ASP 229": "OD1" <-> "OD2" Residue "R ASP 233": "OD1" <-> "OD2" Residue "S ASP 176": "OD1" <-> "OD2" Residue "S ARG 202": "NH1" <-> "NH2" Residue "S ARG 204": "NH1" <-> "NH2" Residue "S ARG 216": "NH1" <-> "NH2" Residue "S GLU 225": "OE1" <-> "OE2" Residue "S TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 238": "OD1" <-> "OD2" Residue "S ARG 240": "NH1" <-> "NH2" Residue "S ARG 241": "NH1" <-> "NH2" Residue "S ASP 256": "OD1" <-> "OD2" Residue "S ARG 262": "NH1" <-> "NH2" Residue "T ASP 176": "OD1" <-> "OD2" Residue "T ARG 202": "NH1" <-> "NH2" Residue "T ARG 204": "NH1" <-> "NH2" Residue "T ARG 216": "NH1" <-> "NH2" Residue "T PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 225": "OE1" <-> "OE2" Residue "T TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 238": "OD1" <-> "OD2" Residue "T ARG 240": "NH1" <-> "NH2" Residue "T ARG 241": "NH1" <-> "NH2" Residue "T ASP 256": "OD1" <-> "OD2" Residue "T ARG 262": "NH1" <-> "NH2" Residue "U ARG 30": "NH1" <-> "NH2" Residue "U ASP 47": "OD1" <-> "OD2" Residue "U GLU 100": "OE1" <-> "OE2" Residue "U GLU 108": "OE1" <-> "OE2" Residue "U ARG 110": "NH1" <-> "NH2" Residue "U ASP 136": "OD1" <-> "OD2" Residue "U ASP 151": "OD1" <-> "OD2" Residue "U GLU 167": "OE1" <-> "OE2" Residue "U GLU 171": "OE1" <-> "OE2" Residue "U ASP 196": "OD1" <-> "OD2" Residue "U ARG 205": "NH1" <-> "NH2" Residue "U GLU 212": "OE1" <-> "OE2" Residue "U ASP 229": "OD1" <-> "OD2" Residue "U ASP 233": "OD1" <-> "OD2" Residue "V ARG 30": "NH1" <-> "NH2" Residue "V ASP 47": "OD1" <-> "OD2" Residue "V GLU 81": "OE1" <-> "OE2" Residue "V GLU 100": "OE1" <-> "OE2" Residue "V GLU 108": "OE1" <-> "OE2" Residue "V ARG 110": "NH1" <-> "NH2" Residue "V ASP 136": "OD1" <-> "OD2" Residue "V ASP 151": "OD1" <-> "OD2" Residue "V GLU 167": "OE1" <-> "OE2" Residue "V GLU 171": "OE1" <-> "OE2" Residue "V ASP 196": "OD1" <-> "OD2" Residue "V ARG 205": "NH1" <-> "NH2" Residue "V GLU 212": "OE1" <-> "OE2" Residue "V ASP 229": "OD1" <-> "OD2" Residue "V ASP 233": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 30327 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "D" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "F" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "G" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "J" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "K" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "M" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "N" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "O" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "P" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "Q" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "R" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "S" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "T" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "U" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "V" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} 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: "D" 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: "G" 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: "J" 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: "K" 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: "M" 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: "N" 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: "Q" 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: "R" 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: "U" 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: "V" 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: 17.69, per 1000 atoms: 0.58 Number of scatterers: 30327 At special positions: 0 Unit cell: (110.818, 116.607, 194.345, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 110 16.00 P 33 15.00 Mg 11 11.99 O 5863 8.00 N 5368 7.00 C 18942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.27 Conformation dependent library (CDL) restraints added in 4.7 seconds 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7216 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 154 helices and 33 sheets defined 30.4% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.863A pdb=" N ARG A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 239 No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'C' and resid 16 through 30 removed outlier: 3.615A pdb=" N ALA C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 49 No H-bonds generated for 'chain 'C' and resid 46 through 49' Processing helix chain 'C' and resid 60 through 65 Processing helix chain 'C' and resid 70 through 73 No H-bonds generated for 'chain 'C' and resid 70 through 73' Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 99 through 112 removed outlier: 3.538A pdb=" N VAL C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 133 removed outlier: 3.758A pdb=" N ALA C 131 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 158 removed outlier: 3.865A pdb=" N MET C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 188 removed outlier: 3.855A pdb=" N THR C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 184 through 188' Processing helix chain 'C' and resid 195 through 201 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 233 through 246 removed outlier: 3.587A pdb=" N ALA C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 242 " --> pdb=" O TYR C 238 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.526A pdb=" N ALA D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 49 No H-bonds generated for 'chain 'D' and resid 46 through 49' Processing helix chain 'D' and resid 60 through 65 Processing helix chain 'D' and resid 70 through 73 No H-bonds generated for 'chain 'D' and resid 70 through 73' Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 99 through 112 removed outlier: 3.541A pdb=" N LYS D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 removed outlier: 3.828A pdb=" N ALA D 131 " --> pdb=" O GLY D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 removed outlier: 3.566A pdb=" N MET D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 188 removed outlier: 3.900A pdb=" N THR D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 184 through 188' Processing helix chain 'D' and resid 195 through 201 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'D' and resid 233 through 246 removed outlier: 3.532A pdb=" N ALA D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 241 removed outlier: 3.863A pdb=" N ARG E 241 " --> pdb=" O GLU E 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 239 No H-bonds generated for 'chain 'F' and resid 236 through 239' Processing helix chain 'G' and resid 16 through 30 removed outlier: 3.616A pdb=" N ALA G 28 " --> pdb=" O GLY G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 49 No H-bonds generated for 'chain 'G' and resid 46 through 49' Processing helix chain 'G' and resid 60 through 65 Processing helix chain 'G' and resid 70 through 73 No H-bonds generated for 'chain 'G' and resid 70 through 73' Processing helix chain 'G' and resid 94 through 96 No H-bonds generated for 'chain 'G' and resid 94 through 96' Processing helix chain 'G' and resid 99 through 112 removed outlier: 3.537A pdb=" N VAL G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 133 removed outlier: 3.758A pdb=" N ALA G 131 " --> pdb=" O GLY G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 158 removed outlier: 3.865A pdb=" N MET G 155 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 188 removed outlier: 3.855A pdb=" N THR G 188 " --> pdb=" O PRO G 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 184 through 188' Processing helix chain 'G' and resid 195 through 201 Processing helix chain 'G' and resid 214 through 222 Processing helix chain 'G' and resid 226 through 228 No H-bonds generated for 'chain 'G' and resid 226 through 228' Processing helix chain 'G' and resid 233 through 246 removed outlier: 3.586A pdb=" N ALA G 241 " --> pdb=" O ALA G 237 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL G 242 " --> pdb=" O TYR G 238 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP G 243 " --> pdb=" O SER G 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 241 removed outlier: 3.863A pdb=" N ARG H 241 " --> pdb=" O GLU H 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 239 No H-bonds generated for 'chain 'I' and resid 236 through 239' Processing helix chain 'J' and resid 16 through 30 removed outlier: 3.615A pdb=" N ALA J 28 " --> pdb=" O GLY J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 49 No H-bonds generated for 'chain 'J' and resid 46 through 49' Processing helix chain 'J' and resid 60 through 65 Processing helix chain 'J' and resid 70 through 73 No H-bonds generated for 'chain 'J' and resid 70 through 73' Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 99 through 112 removed outlier: 3.537A pdb=" N VAL J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP J 112 " --> pdb=" O GLU J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 removed outlier: 3.758A pdb=" N ALA J 131 " --> pdb=" O GLY J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 158 removed outlier: 3.865A pdb=" N MET J 155 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 188 removed outlier: 3.855A pdb=" N THR J 188 " --> pdb=" O PRO J 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 184 through 188' Processing helix chain 'J' and resid 195 through 201 Processing helix chain 'J' and resid 214 through 222 Processing helix chain 'J' and resid 226 through 228 No H-bonds generated for 'chain 'J' and resid 226 through 228' Processing helix chain 'J' and resid 233 through 246 removed outlier: 3.587A pdb=" N ALA J 241 " --> pdb=" O ALA J 237 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL J 242 " --> pdb=" O TYR J 238 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP J 243 " --> pdb=" O SER J 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 30 removed outlier: 3.525A pdb=" N ALA K 28 " --> pdb=" O GLY K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 49 No H-bonds generated for 'chain 'K' and resid 46 through 49' Processing helix chain 'K' and resid 60 through 65 Processing helix chain 'K' and resid 70 through 73 No H-bonds generated for 'chain 'K' and resid 70 through 73' Processing helix chain 'K' and resid 94 through 96 No H-bonds generated for 'chain 'K' and resid 94 through 96' Processing helix chain 'K' and resid 99 through 112 removed outlier: 3.540A pdb=" N LYS K 111 " --> pdb=" O ALA K 107 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP K 112 " --> pdb=" O GLU K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 133 removed outlier: 3.829A pdb=" N ALA K 131 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 158 removed outlier: 3.567A pdb=" N MET K 155 " --> pdb=" O ASP K 151 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY K 157 " --> pdb=" O ASP K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 188 removed outlier: 3.900A pdb=" N THR K 188 " --> pdb=" O PRO K 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 184 through 188' Processing helix chain 'K' and resid 195 through 201 Processing helix chain 'K' and resid 214 through 222 Processing helix chain 'K' and resid 226 through 228 No H-bonds generated for 'chain 'K' and resid 226 through 228' Processing helix chain 'K' and resid 233 through 246 removed outlier: 3.532A pdb=" N ALA K 241 " --> pdb=" O ALA K 237 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP K 243 " --> pdb=" O SER K 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 239 No H-bonds generated for 'chain 'L' and resid 236 through 239' Processing helix chain 'M' and resid 16 through 30 removed outlier: 3.615A pdb=" N ALA M 28 " --> pdb=" O GLY M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 49 No H-bonds generated for 'chain 'M' and resid 46 through 49' Processing helix chain 'M' and resid 60 through 65 Processing helix chain 'M' and resid 70 through 73 No H-bonds generated for 'chain 'M' and resid 70 through 73' Processing helix chain 'M' and resid 94 through 96 No H-bonds generated for 'chain 'M' and resid 94 through 96' Processing helix chain 'M' and resid 99 through 112 removed outlier: 3.537A pdb=" N VAL M 105 " --> pdb=" O GLY M 101 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP M 112 " --> pdb=" O GLU M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 133 removed outlier: 3.759A pdb=" N ALA M 131 " --> pdb=" O GLY M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 158 removed outlier: 3.865A pdb=" N MET M 155 " --> pdb=" O ASP M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 188 removed outlier: 3.855A pdb=" N THR M 188 " --> pdb=" O PRO M 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 184 through 188' Processing helix chain 'M' and resid 195 through 201 Processing helix chain 'M' and resid 214 through 222 Processing helix chain 'M' and resid 226 through 228 No H-bonds generated for 'chain 'M' and resid 226 through 228' Processing helix chain 'M' and resid 233 through 246 removed outlier: 3.587A pdb=" N ALA M 241 " --> pdb=" O ALA M 237 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL M 242 " --> pdb=" O TYR M 238 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP M 243 " --> pdb=" O SER M 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 30 removed outlier: 3.526A pdb=" N ALA N 28 " --> pdb=" O GLY N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 49 No H-bonds generated for 'chain 'N' and resid 46 through 49' Processing helix chain 'N' and resid 60 through 65 Processing helix chain 'N' and resid 70 through 73 No H-bonds generated for 'chain 'N' and resid 70 through 73' Processing helix chain 'N' and resid 94 through 96 No H-bonds generated for 'chain 'N' and resid 94 through 96' Processing helix chain 'N' and resid 99 through 112 removed outlier: 3.540A pdb=" N LYS N 111 " --> pdb=" O ALA N 107 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP N 112 " --> pdb=" O GLU N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 133 removed outlier: 3.828A pdb=" N ALA N 131 " --> pdb=" O GLY N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 158 removed outlier: 3.566A pdb=" N MET N 155 " --> pdb=" O ASP N 151 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY N 157 " --> pdb=" O ASP N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 188 removed outlier: 3.900A pdb=" N THR N 188 " --> pdb=" O PRO N 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 184 through 188' Processing helix chain 'N' and resid 195 through 201 Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 226 through 228 No H-bonds generated for 'chain 'N' and resid 226 through 228' Processing helix chain 'N' and resid 233 through 246 removed outlier: 3.531A pdb=" N ALA N 241 " --> pdb=" O ALA N 237 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP N 243 " --> pdb=" O SER N 239 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 241 removed outlier: 3.863A pdb=" N ARG O 241 " --> pdb=" O GLU O 237 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 239 No H-bonds generated for 'chain 'P' and resid 236 through 239' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.616A pdb=" N ALA Q 28 " --> pdb=" O GLY Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 49 No H-bonds generated for 'chain 'Q' and resid 46 through 49' Processing helix chain 'Q' and resid 60 through 65 Processing helix chain 'Q' and resid 70 through 73 No H-bonds generated for 'chain 'Q' and resid 70 through 73' Processing helix chain 'Q' and resid 94 through 96 No H-bonds generated for 'chain 'Q' and resid 94 through 96' Processing helix chain 'Q' and resid 99 through 112 removed outlier: 3.537A pdb=" N VAL Q 105 " --> pdb=" O GLY Q 101 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP Q 112 " --> pdb=" O GLU Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 133 removed outlier: 3.758A pdb=" N ALA Q 131 " --> pdb=" O GLY Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 158 removed outlier: 3.865A pdb=" N MET Q 155 " --> pdb=" O ASP Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 184 through 188 removed outlier: 3.855A pdb=" N THR Q 188 " --> pdb=" O PRO Q 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 184 through 188' Processing helix chain 'Q' and resid 195 through 201 Processing helix chain 'Q' and resid 214 through 222 Processing helix chain 'Q' and resid 226 through 228 No H-bonds generated for 'chain 'Q' and resid 226 through 228' Processing helix chain 'Q' and resid 233 through 246 removed outlier: 3.587A pdb=" N ALA Q 241 " --> pdb=" O ALA Q 237 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL Q 242 " --> pdb=" O TYR Q 238 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP Q 243 " --> pdb=" O SER Q 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 30 removed outlier: 3.525A pdb=" N ALA R 28 " --> pdb=" O GLY R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 49 No H-bonds generated for 'chain 'R' and resid 46 through 49' Processing helix chain 'R' and resid 60 through 65 Processing helix chain 'R' and resid 70 through 73 No H-bonds generated for 'chain 'R' and resid 70 through 73' Processing helix chain 'R' and resid 94 through 96 No H-bonds generated for 'chain 'R' and resid 94 through 96' Processing helix chain 'R' and resid 99 through 112 removed outlier: 3.541A pdb=" N LYS R 111 " --> pdb=" O ALA R 107 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP R 112 " --> pdb=" O GLU R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 removed outlier: 3.828A pdb=" N ALA R 131 " --> pdb=" O GLY R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 158 removed outlier: 3.565A pdb=" N MET R 155 " --> pdb=" O ASP R 151 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY R 157 " --> pdb=" O ASP R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 188 removed outlier: 3.900A pdb=" N THR R 188 " --> pdb=" O PRO R 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 184 through 188' Processing helix chain 'R' and resid 195 through 201 Processing helix chain 'R' and resid 214 through 222 Processing helix chain 'R' and resid 226 through 228 No H-bonds generated for 'chain 'R' and resid 226 through 228' Processing helix chain 'R' and resid 233 through 246 removed outlier: 3.531A pdb=" N ALA R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP R 243 " --> pdb=" O SER R 239 " (cutoff:3.500A) Processing helix chain 'S' and resid 236 through 241 removed outlier: 3.863A pdb=" N ARG S 241 " --> pdb=" O GLU S 237 " (cutoff:3.500A) Processing helix chain 'T' and resid 236 through 239 No H-bonds generated for 'chain 'T' and resid 236 through 239' Processing helix chain 'U' and resid 16 through 30 removed outlier: 3.615A pdb=" N ALA U 28 " --> pdb=" O GLY U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 49 No H-bonds generated for 'chain 'U' and resid 46 through 49' Processing helix chain 'U' and resid 60 through 65 Processing helix chain 'U' and resid 70 through 73 No H-bonds generated for 'chain 'U' and resid 70 through 73' Processing helix chain 'U' and resid 94 through 96 No H-bonds generated for 'chain 'U' and resid 94 through 96' Processing helix chain 'U' and resid 99 through 112 removed outlier: 3.537A pdb=" N VAL U 105 " --> pdb=" O GLY U 101 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP U 112 " --> pdb=" O GLU U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 126 through 133 removed outlier: 3.758A pdb=" N ALA U 131 " --> pdb=" O GLY U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 158 removed outlier: 3.865A pdb=" N MET U 155 " --> pdb=" O ASP U 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 184 through 188 removed outlier: 3.855A pdb=" N THR U 188 " --> pdb=" O PRO U 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 184 through 188' Processing helix chain 'U' and resid 195 through 201 Processing helix chain 'U' and resid 214 through 222 Processing helix chain 'U' and resid 226 through 228 No H-bonds generated for 'chain 'U' and resid 226 through 228' Processing helix chain 'U' and resid 233 through 246 removed outlier: 3.587A pdb=" N ALA U 241 " --> pdb=" O ALA U 237 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL U 242 " --> pdb=" O TYR U 238 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP U 243 " --> pdb=" O SER U 239 " (cutoff:3.500A) Processing helix chain 'V' and resid 16 through 30 removed outlier: 3.525A pdb=" N ALA V 28 " --> pdb=" O GLY V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 49 No H-bonds generated for 'chain 'V' and resid 46 through 49' Processing helix chain 'V' and resid 60 through 65 Processing helix chain 'V' and resid 70 through 73 No H-bonds generated for 'chain 'V' and resid 70 through 73' Processing helix chain 'V' and resid 94 through 96 No H-bonds generated for 'chain 'V' and resid 94 through 96' Processing helix chain 'V' and resid 99 through 112 removed outlier: 3.540A pdb=" N LYS V 111 " --> pdb=" O ALA V 107 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP V 112 " --> pdb=" O GLU V 108 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 133 removed outlier: 3.828A pdb=" N ALA V 131 " --> pdb=" O GLY V 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 146 through 158 removed outlier: 3.566A pdb=" N MET V 155 " --> pdb=" O ASP V 151 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY V 157 " --> pdb=" O ASP V 153 " (cutoff:3.500A) Processing helix chain 'V' and resid 184 through 188 removed outlier: 3.900A pdb=" N THR V 188 " --> pdb=" O PRO V 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 184 through 188' Processing helix chain 'V' and resid 195 through 201 Processing helix chain 'V' and resid 214 through 222 Processing helix chain 'V' and resid 226 through 228 No H-bonds generated for 'chain 'V' and resid 226 through 228' Processing helix chain 'V' and resid 233 through 246 removed outlier: 3.532A pdb=" N ALA V 241 " --> pdb=" O ALA V 237 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP V 243 " --> pdb=" O SER V 239 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 158 through 160 Processing sheet with id= B, first strand: chain 'A' and resid 169 through 172 removed outlier: 6.811A pdb=" N GLU A 188 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ALA A 172 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU A 190 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG A 204 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA A 191 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU A 206 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU A 226 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ALA A 207 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N SER A 228 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 158 through 160 Processing sheet with id= D, first strand: chain 'B' and resid 169 through 172 removed outlier: 6.634A pdb=" N GLU B 188 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ALA B 172 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU B 190 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG B 204 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ALA B 191 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 206 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B 226 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ALA B 207 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER B 228 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 206 through 209 removed outlier: 7.245A pdb=" N LEU C 207 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU C 177 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL C 209 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU C 179 " --> pdb=" O VAL C 209 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 206 through 209 removed outlier: 7.420A pdb=" N LEU D 207 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU D 177 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL D 209 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU D 179 " --> pdb=" O VAL D 209 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 158 through 160 Processing sheet with id= H, first strand: chain 'E' and resid 169 through 172 removed outlier: 6.812A pdb=" N GLU E 188 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ALA E 172 " --> pdb=" O GLU E 188 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU E 190 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG E 204 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA E 191 " --> pdb=" O ARG E 204 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU E 206 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU E 226 " --> pdb=" O ALA E 205 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ALA E 207 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER E 228 " --> pdb=" O ALA E 207 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 158 through 160 Processing sheet with id= J, first strand: chain 'F' and resid 169 through 172 removed outlier: 6.634A pdb=" N GLU F 188 " --> pdb=" O ILE F 170 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ALA F 172 " --> pdb=" O GLU F 188 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU F 190 " --> pdb=" O ALA F 172 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG F 204 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ALA F 191 " --> pdb=" O ARG F 204 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU F 206 " --> pdb=" O ALA F 191 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU F 226 " --> pdb=" O ALA F 205 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA F 207 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N SER F 228 " --> pdb=" O ALA F 207 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 206 through 209 removed outlier: 7.245A pdb=" N LEU G 207 " --> pdb=" O GLU G 175 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU G 177 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL G 209 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU G 179 " --> pdb=" O VAL G 209 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 158 through 160 Processing sheet with id= M, first strand: chain 'H' and resid 169 through 172 removed outlier: 6.811A pdb=" N GLU H 188 " --> pdb=" O ILE H 170 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ALA H 172 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU H 190 " --> pdb=" O ALA H 172 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG H 204 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA H 191 " --> pdb=" O ARG H 204 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU H 206 " --> pdb=" O ALA H 191 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU H 226 " --> pdb=" O ALA H 205 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ALA H 207 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N SER H 228 " --> pdb=" O ALA H 207 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 158 through 160 Processing sheet with id= O, first strand: chain 'I' and resid 169 through 172 removed outlier: 6.634A pdb=" N GLU I 188 " --> pdb=" O ILE I 170 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ALA I 172 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU I 190 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG I 204 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ALA I 191 " --> pdb=" O ARG I 204 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU I 206 " --> pdb=" O ALA I 191 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU I 226 " --> pdb=" O ALA I 205 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA I 207 " --> pdb=" O LEU I 226 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER I 228 " --> pdb=" O ALA I 207 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 206 through 209 removed outlier: 7.244A pdb=" N LEU J 207 " --> pdb=" O GLU J 175 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU J 177 " --> pdb=" O LEU J 207 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL J 209 " --> pdb=" O LEU J 177 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU J 179 " --> pdb=" O VAL J 209 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 206 through 209 removed outlier: 7.421A pdb=" N LEU K 207 " --> pdb=" O GLU K 175 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU K 177 " --> pdb=" O LEU K 207 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL K 209 " --> pdb=" O LEU K 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU K 179 " --> pdb=" O VAL K 209 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 158 through 160 Processing sheet with id= S, first strand: chain 'L' and resid 169 through 172 removed outlier: 6.633A pdb=" N GLU L 188 " --> pdb=" O ILE L 170 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ALA L 172 " --> pdb=" O GLU L 188 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU L 190 " --> pdb=" O ALA L 172 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG L 204 " --> pdb=" O LEU L 189 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ALA L 191 " --> pdb=" O ARG L 204 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU L 206 " --> pdb=" O ALA L 191 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU L 226 " --> pdb=" O ALA L 205 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA L 207 " --> pdb=" O LEU L 226 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER L 228 " --> pdb=" O ALA L 207 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'M' and resid 206 through 209 removed outlier: 7.245A pdb=" N LEU M 207 " --> pdb=" O GLU M 175 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU M 177 " --> pdb=" O LEU M 207 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL M 209 " --> pdb=" O LEU M 177 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU M 179 " --> pdb=" O VAL M 209 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'N' and resid 206 through 209 removed outlier: 7.420A pdb=" N LEU N 207 " --> pdb=" O GLU N 175 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU N 177 " --> pdb=" O LEU N 207 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL N 209 " --> pdb=" O LEU N 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU N 179 " --> pdb=" O VAL N 209 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 158 through 160 Processing sheet with id= W, first strand: chain 'O' and resid 169 through 172 removed outlier: 6.811A pdb=" N GLU O 188 " --> pdb=" O ILE O 170 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ALA O 172 " --> pdb=" O GLU O 188 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU O 190 " --> pdb=" O ALA O 172 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG O 204 " --> pdb=" O LEU O 189 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA O 191 " --> pdb=" O ARG O 204 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU O 206 " --> pdb=" O ALA O 191 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU O 226 " --> pdb=" O ALA O 205 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ALA O 207 " --> pdb=" O LEU O 226 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N SER O 228 " --> pdb=" O ALA O 207 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'P' and resid 158 through 160 Processing sheet with id= Y, first strand: chain 'P' and resid 169 through 172 removed outlier: 6.633A pdb=" N GLU P 188 " --> pdb=" O ILE P 170 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ALA P 172 " --> pdb=" O GLU P 188 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU P 190 " --> pdb=" O ALA P 172 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG P 204 " --> pdb=" O LEU P 189 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ALA P 191 " --> pdb=" O ARG P 204 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU P 206 " --> pdb=" O ALA P 191 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU P 226 " --> pdb=" O ALA P 205 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA P 207 " --> pdb=" O LEU P 226 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER P 228 " --> pdb=" O ALA P 207 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Q' and resid 206 through 209 removed outlier: 7.245A pdb=" N LEU Q 207 " --> pdb=" O GLU Q 175 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU Q 177 " --> pdb=" O LEU Q 207 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL Q 209 " --> pdb=" O LEU Q 177 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU Q 179 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'R' and resid 206 through 209 removed outlier: 7.421A pdb=" N LEU R 207 " --> pdb=" O GLU R 175 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU R 177 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL R 209 " --> pdb=" O LEU R 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU R 179 " --> pdb=" O VAL R 209 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'S' and resid 158 through 160 Processing sheet with id= AC, first strand: chain 'S' and resid 169 through 172 removed outlier: 6.811A pdb=" N GLU S 188 " --> pdb=" O ILE S 170 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ALA S 172 " --> pdb=" O GLU S 188 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU S 190 " --> pdb=" O ALA S 172 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG S 204 " --> pdb=" O LEU S 189 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA S 191 " --> pdb=" O ARG S 204 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU S 206 " --> pdb=" O ALA S 191 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU S 226 " --> pdb=" O ALA S 205 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ALA S 207 " --> pdb=" O LEU S 226 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N SER S 228 " --> pdb=" O ALA S 207 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'T' and resid 158 through 160 Processing sheet with id= AE, first strand: chain 'T' and resid 169 through 172 removed outlier: 6.634A pdb=" N GLU T 188 " --> pdb=" O ILE T 170 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ALA T 172 " --> pdb=" O GLU T 188 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU T 190 " --> pdb=" O ALA T 172 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG T 204 " --> pdb=" O LEU T 189 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ALA T 191 " --> pdb=" O ARG T 204 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU T 206 " --> pdb=" O ALA T 191 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU T 226 " --> pdb=" O ALA T 205 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA T 207 " --> pdb=" O LEU T 226 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER T 228 " --> pdb=" O ALA T 207 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'U' and resid 206 through 209 removed outlier: 7.245A pdb=" N LEU U 207 " --> pdb=" O GLU U 175 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU U 177 " --> pdb=" O LEU U 207 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL U 209 " --> pdb=" O LEU U 177 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU U 179 " --> pdb=" O VAL U 209 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'V' and resid 206 through 209 removed outlier: 7.420A pdb=" N LEU V 207 " --> pdb=" O GLU V 175 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU V 177 " --> pdb=" O LEU V 207 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL V 209 " --> pdb=" O LEU V 177 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU V 179 " --> pdb=" O VAL V 209 " (cutoff:3.500A) 995 hydrogen bonds defined for protein. 2820 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: 11.81 Time building geometry restraints manager: 13.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10271 1.34 - 1.46: 5541 1.46 - 1.58: 14647 1.58 - 1.70: 55 1.70 - 1.82: 187 Bond restraints: 30701 Sorted by residual: bond pdb=" C4 ATP D 302 " pdb=" C5 ATP D 302 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.59e+01 bond pdb=" C4 ATP R 302 " pdb=" C5 ATP R 302 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.54e+01 bond pdb=" C4 ATP K 302 " pdb=" C5 ATP K 302 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.53e+01 bond pdb=" C4 ATP V 302 " pdb=" C5 ATP V 302 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.51e+01 bond pdb=" C4 ATP N 302 " pdb=" C5 ATP N 302 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 ... (remaining 30696 not shown) Histogram of bond angle deviations from ideal: 97.16 - 104.94: 515 104.94 - 112.72: 16995 112.72 - 120.50: 13083 120.50 - 128.28: 10810 128.28 - 136.05: 155 Bond angle restraints: 41558 Sorted by residual: angle pdb=" PB ATP V 302 " pdb=" O3B ATP V 302 " pdb=" PG ATP V 302 " ideal model delta sigma weight residual 139.87 118.90 20.97 1.00e+00 1.00e+00 4.40e+02 angle pdb=" PB ATP D 302 " pdb=" O3B ATP D 302 " pdb=" PG ATP D 302 " ideal model delta sigma weight residual 139.87 118.91 20.96 1.00e+00 1.00e+00 4.39e+02 angle pdb=" PB ATP R 302 " pdb=" O3B ATP R 302 " pdb=" PG ATP R 302 " ideal model delta sigma weight residual 139.87 118.92 20.95 1.00e+00 1.00e+00 4.39e+02 angle pdb=" PB ATP N 302 " pdb=" O3B ATP N 302 " pdb=" PG ATP N 302 " ideal model delta sigma weight residual 139.87 118.92 20.95 1.00e+00 1.00e+00 4.39e+02 angle pdb=" PB ATP K 302 " pdb=" O3B ATP K 302 " pdb=" PG ATP K 302 " ideal model delta sigma weight residual 139.87 118.92 20.95 1.00e+00 1.00e+00 4.39e+02 ... (remaining 41553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 16639 17.27 - 34.54: 1555 34.54 - 51.80: 303 51.80 - 69.07: 82 69.07 - 86.34: 44 Dihedral angle restraints: 18623 sinusoidal: 7370 harmonic: 11253 Sorted by residual: dihedral pdb=" CA MET G 132 " pdb=" C MET G 132 " pdb=" N TYR G 133 " pdb=" CA TYR G 133 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA MET C 132 " pdb=" C MET C 132 " pdb=" N TYR C 133 " pdb=" CA TYR C 133 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA MET U 132 " pdb=" C MET U 132 " pdb=" N TYR U 133 " pdb=" CA TYR U 133 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 18620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2462 0.031 - 0.063: 1485 0.063 - 0.094: 538 0.094 - 0.126: 299 0.126 - 0.157: 133 Chirality restraints: 4917 Sorted by residual: chirality pdb=" CA ILE P 195 " pdb=" N ILE P 195 " pdb=" C ILE P 195 " pdb=" CB ILE P 195 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CA ILE L 195 " pdb=" N ILE L 195 " pdb=" C ILE L 195 " pdb=" CB ILE L 195 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA ILE T 195 " pdb=" N ILE T 195 " pdb=" C ILE T 195 " pdb=" CB ILE T 195 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 4914 not shown) Planarity restraints: 5313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL M 224 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO M 225 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO M 225 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO M 225 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 224 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO C 225 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 225 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 225 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL U 224 " 0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO U 225 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO U 225 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO U 225 " 0.022 5.00e-02 4.00e+02 ... (remaining 5310 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 251 2.58 - 3.16: 23579 3.16 - 3.74: 45810 3.74 - 4.32: 70021 4.32 - 4.90: 115972 Nonbonded interactions: 255633 Sorted by model distance: nonbonded pdb=" OG1 THR J 17 " pdb="MG MG J 301 " model vdw 2.001 2.170 nonbonded pdb=" OG1 THR U 17 " pdb="MG MG U 301 " model vdw 2.001 2.170 nonbonded pdb=" OG1 THR M 17 " pdb="MG MG M 301 " model vdw 2.001 2.170 nonbonded pdb=" OG1 THR Q 17 " pdb="MG MG Q 301 " model vdw 2.001 2.170 nonbonded pdb=" OG1 THR C 17 " pdb="MG MG C 301 " model vdw 2.001 2.170 ... (remaining 255628 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' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 33 5.49 5 Mg 11 5.21 5 S 110 5.16 5 C 18942 2.51 5 N 5368 2.21 5 O 5863 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 6.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 27.660 Check model and map are aligned: 0.430 Process input model: 78.450 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Set scattering table: 0.280 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.006 0.081 30701 Z= 0.388 Angle : 1.004 20.967 41558 Z= 0.684 Chirality : 0.052 0.157 4917 Planarity : 0.004 0.039 5313 Dihedral : 14.774 86.339 11407 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.10), residues: 3927 helix: -4.03 (0.07), residues: 1320 sheet: -2.32 (0.15), residues: 935 loop : -1.99 (0.13), residues: 1672 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 704 time to evaluate : 3.868 Fit side-chains 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: 704 average time/residue: 0.5345 time to fit residues: 554.4367 Evaluate side-chains 446 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 3.663 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 0.8980 chunk 291 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 196 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 301 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 349 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS B 250 HIS C 143 ASN D 62 ASN F 250 HIS F 259 ASN G 45 ASN G 65 ASN G 129 HIS I 259 ASN J 65 ASN J 129 HIS J 143 ASN K 62 ASN M 72 GLN M 129 HIS M 143 ASN N 45 ASN N 62 ASN N 143 ASN O 250 HIS P 259 ASN Q 129 HIS Q 143 ASN R 62 ASN T 169 GLN T 250 HIS T 259 ASN U 129 HIS U 143 ASN V 62 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 30701 Z= 0.201 Angle : 0.558 11.000 41558 Z= 0.286 Chirality : 0.045 0.177 4917 Planarity : 0.004 0.046 5313 Dihedral : 5.619 43.001 4312 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.12), residues: 3927 helix: -2.15 (0.12), residues: 1309 sheet: -1.31 (0.17), residues: 869 loop : -1.70 (0.13), residues: 1749 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 500 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 65 residues processed: 584 average time/residue: 0.4724 time to fit residues: 423.0210 Evaluate side-chains 472 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 407 time to evaluate : 3.518 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.2755 time to fit residues: 38.9614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 350 optimal weight: 0.4980 chunk 378 optimal weight: 1.9990 chunk 311 optimal weight: 1.9990 chunk 347 optimal weight: 4.9990 chunk 119 optimal weight: 0.0470 chunk 280 optimal weight: 1.9990 overall best weight: 1.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN F 259 ASN H 259 ASN J 129 HIS L 259 ASN M 176 HIS N 45 ASN N 176 HIS O 259 ASN Q 72 GLN R 176 HIS ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 259 ASN U 65 ASN U 72 GLN U 143 ASN V 129 HIS V 176 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 30701 Z= 0.247 Angle : 0.564 8.287 41558 Z= 0.285 Chirality : 0.045 0.170 4917 Planarity : 0.004 0.039 5313 Dihedral : 5.850 54.872 4312 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.12), residues: 3927 helix: -1.39 (0.13), residues: 1309 sheet: -1.20 (0.15), residues: 1034 loop : -1.51 (0.14), residues: 1584 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 449 time to evaluate : 3.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 53 residues processed: 506 average time/residue: 0.4838 time to fit residues: 376.9527 Evaluate side-chains 437 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 384 time to evaluate : 3.746 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.2827 time to fit residues: 33.2980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 0.9990 chunk 263 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 235 optimal weight: 4.9990 chunk 351 optimal weight: 0.0040 chunk 372 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 333 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN C 72 GLN E 250 HIS F 259 ASN I 259 ASN J 84 HIS K 72 GLN M 176 HIS N 45 ASN P 250 HIS Q 176 HIS R 176 HIS ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 259 ASN U 65 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 30701 Z= 0.273 Angle : 0.571 9.366 41558 Z= 0.287 Chirality : 0.045 0.172 4917 Planarity : 0.004 0.043 5313 Dihedral : 5.864 53.700 4312 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.12), residues: 3927 helix: -1.13 (0.13), residues: 1309 sheet: -1.00 (0.16), residues: 1023 loop : -1.49 (0.14), residues: 1595 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 404 time to evaluate : 4.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 50 residues processed: 475 average time/residue: 0.5040 time to fit residues: 368.9603 Evaluate side-chains 424 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 374 time to evaluate : 3.392 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.2705 time to fit residues: 30.4471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 309 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 277 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 317 optimal weight: 0.9980 chunk 257 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 chunk 334 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 176 HIS N 45 ASN Q 65 ASN Q 176 HIS Q 222 GLN R 176 HIS ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 259 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 30701 Z= 0.213 Angle : 0.526 8.253 41558 Z= 0.265 Chirality : 0.044 0.164 4917 Planarity : 0.003 0.044 5313 Dihedral : 5.534 48.818 4312 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3927 helix: -0.81 (0.14), residues: 1309 sheet: -0.83 (0.16), residues: 1023 loop : -1.39 (0.14), residues: 1595 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 414 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 28 residues processed: 447 average time/residue: 0.4985 time to fit residues: 338.4510 Evaluate side-chains 399 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 371 time to evaluate : 3.559 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2889 time to fit residues: 20.0863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 0.0060 chunk 335 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 372 optimal weight: 3.9990 chunk 309 optimal weight: 0.9980 chunk 172 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** H 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 176 HIS Q 176 HIS R 176 HIS R 222 GLN T 259 ASN ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 30701 Z= 0.227 Angle : 0.537 8.512 41558 Z= 0.269 Chirality : 0.044 0.164 4917 Planarity : 0.003 0.046 5313 Dihedral : 5.514 48.254 4312 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.13), residues: 3927 helix: -0.70 (0.14), residues: 1320 sheet: -0.63 (0.17), residues: 869 loop : -1.26 (0.14), residues: 1738 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 381 time to evaluate : 3.673 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 41 residues processed: 423 average time/residue: 0.5716 time to fit residues: 376.7371 Evaluate side-chains 409 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 368 time to evaluate : 3.585 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.3702 time to fit residues: 32.2379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 chunk 210 optimal weight: 0.5980 chunk 313 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 chunk 371 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 226 optimal weight: 0.0070 chunk 171 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN C 222 GLN ** H 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN R 176 HIS T 259 ASN ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 176 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 30701 Z= 0.151 Angle : 0.484 7.436 41558 Z= 0.244 Chirality : 0.043 0.157 4917 Planarity : 0.003 0.047 5313 Dihedral : 5.080 42.512 4312 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3927 helix: -0.32 (0.14), residues: 1309 sheet: -0.70 (0.16), residues: 1034 loop : -1.27 (0.14), residues: 1584 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 402 time to evaluate : 3.245 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 422 average time/residue: 0.4482 time to fit residues: 292.5982 Evaluate side-chains 376 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 366 time to evaluate : 3.437 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2698 time to fit residues: 9.9272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 34 optimal weight: 0.1980 chunk 291 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 GLN D 84 HIS ** H 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 259 ASN J 143 ASN J 176 HIS M 129 HIS M 143 ASN M 176 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN Q 84 HIS Q 176 HIS ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 84 HIS R 176 HIS T 259 ASN ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 176 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 30701 Z= 0.325 Angle : 0.610 9.588 41558 Z= 0.303 Chirality : 0.047 0.168 4917 Planarity : 0.004 0.048 5313 Dihedral : 5.820 51.316 4312 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.13), residues: 3927 helix: -0.57 (0.14), residues: 1320 sheet: -0.61 (0.17), residues: 869 loop : -1.21 (0.14), residues: 1738 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 373 time to evaluate : 3.715 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 28 residues processed: 405 average time/residue: 0.5286 time to fit residues: 326.0389 Evaluate side-chains 386 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 358 time to evaluate : 3.494 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2881 time to fit residues: 20.6421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 3.9990 chunk 355 optimal weight: 0.4980 chunk 324 optimal weight: 0.8980 chunk 345 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 271 optimal weight: 0.0870 chunk 106 optimal weight: 20.0000 chunk 312 optimal weight: 3.9990 chunk 327 optimal weight: 2.9990 chunk 344 optimal weight: 4.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN G 84 HIS ** H 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 221 GLN M 176 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN Q 176 HIS R 176 HIS ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 30701 Z= 0.235 Angle : 0.546 8.731 41558 Z= 0.273 Chirality : 0.044 0.164 4917 Planarity : 0.003 0.049 5313 Dihedral : 5.551 47.697 4312 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 3927 helix: -0.43 (0.14), residues: 1320 sheet: -0.54 (0.17), residues: 869 loop : -1.18 (0.14), residues: 1738 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 368 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 17 residues processed: 380 average time/residue: 0.5640 time to fit residues: 332.0982 Evaluate side-chains 367 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 350 time to evaluate : 3.844 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3875 time to fit residues: 17.0838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 0.0970 chunk 365 optimal weight: 0.9980 chunk 223 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 254 optimal weight: 5.9990 chunk 383 optimal weight: 0.4980 chunk 353 optimal weight: 0.0870 chunk 305 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 235 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN C 222 GLN ** H 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 259 ASN K 222 GLN ** M 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 222 GLN R 222 GLN T 259 ASN ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 176 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 30701 Z= 0.131 Angle : 0.475 7.036 41558 Z= 0.240 Chirality : 0.042 0.155 4917 Planarity : 0.003 0.050 5313 Dihedral : 4.859 39.729 4312 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 3927 helix: -0.04 (0.15), residues: 1320 sheet: -0.54 (0.17), residues: 957 loop : -1.12 (0.14), residues: 1650 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 390 time to evaluate : 3.664 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 391 average time/residue: 0.4951 time to fit residues: 295.0266 Evaluate side-chains 365 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 362 time to evaluate : 3.690 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2980 time to fit residues: 6.7232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 242 optimal weight: 2.9990 chunk 325 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 281 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 305 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 314 optimal weight: 0.0070 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 GLN G 222 GLN K 222 GLN M 176 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 259 ASN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 HIS T 259 ASN ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 176 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.153059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.124122 restraints weight = 34519.894| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.63 r_work: 0.3169 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 30701 Z= 0.321 Angle : 0.601 9.085 41558 Z= 0.298 Chirality : 0.047 0.172 4917 Planarity : 0.004 0.050 5313 Dihedral : 5.697 49.761 4312 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.13), residues: 3927 helix: -0.31 (0.14), residues: 1320 sheet: -0.70 (0.16), residues: 1034 loop : -1.14 (0.15), residues: 1573 =============================================================================== Job complete usr+sys time: 7566.63 seconds wall clock time: 139 minutes 43.94 seconds (8383.94 seconds total)