Starting phenix.real_space_refine on Thu Mar 21 15:41:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riq_4897/03_2024/6riq_4897_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riq_4897/03_2024/6riq_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_4897/03_2024/6riq_4897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riq_4897/03_2024/6riq_4897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riq_4897/03_2024/6riq_4897_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riq_4897/03_2024/6riq_4897_neut_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 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. 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 16.70, per 1000 atoms: 0.55 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: 12.10 Conformation dependent library (CDL) restraints added in 5.7 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: 7.06 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: 12.20 Time building geometry restraints manager: 13.02 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: 16760 17.27 - 34.54: 1704 34.54 - 51.80: 341 51.80 - 69.07: 115 69.07 - 86.34: 44 Dihedral angle restraints: 18964 sinusoidal: 7711 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 18961 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 25.690 Check model and map are aligned: 0.540 Set scattering table: 0.300 Process input model: 85.020 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 15.466 86.339 11748 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 % Allowed : 12.95 % Favored : 87.05 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP T 245 HIS 0.006 0.001 HIS E 250 PHE 0.021 0.003 PHE D 60 TYR 0.016 0.002 TYR R 182 ARG 0.006 0.001 ARG G 181 *********************** 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 : 3.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 262 ARG cc_start: 0.8208 (tmt-80) cc_final: 0.7979 (tpt90) REVERT: C 189 LYS cc_start: 0.7669 (mtpp) cc_final: 0.7413 (mttm) REVERT: D 162 LYS cc_start: 0.7798 (mtpt) cc_final: 0.7562 (mmtp) REVERT: D 168 LYS cc_start: 0.7676 (mtmt) cc_final: 0.7088 (mttp) REVERT: E 241 ARG cc_start: 0.7108 (ttm-80) cc_final: 0.6829 (mtm-85) REVERT: G 93 ASP cc_start: 0.6104 (p0) cc_final: 0.5451 (t0) REVERT: G 94 LYS cc_start: 0.5047 (mtmm) cc_final: 0.4687 (pttt) REVERT: G 112 ASP cc_start: 0.7034 (m-30) cc_final: 0.6773 (m-30) REVERT: G 192 MET cc_start: 0.7280 (mtp) cc_final: 0.7006 (mtp) REVERT: G 253 ARG cc_start: 0.4927 (mtm180) cc_final: 0.3691 (mtt-85) REVERT: H 192 ASP cc_start: 0.7455 (p0) cc_final: 0.6994 (t0) REVERT: H 241 ARG cc_start: 0.7133 (ttm-80) cc_final: 0.6876 (ttm110) REVERT: J 77 ASP cc_start: 0.7640 (m-30) cc_final: 0.7264 (t0) REVERT: J 193 LEU cc_start: 0.7922 (mt) cc_final: 0.7680 (mp) REVERT: J 197 ASP cc_start: 0.7477 (m-30) cc_final: 0.7178 (m-30) REVERT: J 231 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7964 (mm110) REVERT: K 65 ASN cc_start: 0.7608 (m-40) cc_final: 0.7341 (m110) REVERT: K 162 LYS cc_start: 0.7029 (mtpt) cc_final: 0.6795 (mmtt) REVERT: K 176 HIS cc_start: 0.6933 (m-70) cc_final: 0.6431 (m170) REVERT: M 50 MET cc_start: 0.8117 (mmm) cc_final: 0.7771 (tpt) REVERT: M 78 LYS cc_start: 0.7513 (pttp) cc_final: 0.6996 (mmtt) REVERT: M 95 ASP cc_start: 0.7571 (p0) cc_final: 0.6925 (t0) REVERT: N 53 GLU cc_start: 0.8315 (pt0) cc_final: 0.8009 (pt0) REVERT: N 112 ASP cc_start: 0.6655 (m-30) cc_final: 0.6414 (m-30) REVERT: N 162 LYS cc_start: 0.7820 (mtpt) cc_final: 0.7499 (mttt) REVERT: N 168 LYS cc_start: 0.7749 (mtmt) cc_final: 0.7434 (mtpp) REVERT: N 199 GLU cc_start: 0.8156 (tt0) cc_final: 0.7500 (tp30) REVERT: O 161 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8289 (mtpt) REVERT: O 233 TYR cc_start: 0.8930 (p90) cc_final: 0.8593 (p90) REVERT: P 204 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7784 (mtm180) REVERT: Q 3 LYS cc_start: 0.7559 (ttmm) cc_final: 0.7039 (mttp) REVERT: R 3 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7694 (tppt) REVERT: R 162 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7587 (mtmt) REVERT: T 204 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7695 (mtm180) REVERT: T 240 ARG cc_start: 0.8075 (mtp-110) cc_final: 0.7387 (mtt180) REVERT: T 262 ARG cc_start: 0.8240 (tmt-80) cc_final: 0.7970 (tpp80) REVERT: U 155 MET cc_start: 0.7871 (tpp) cc_final: 0.7664 (tpt) REVERT: U 192 MET cc_start: 0.8768 (mtp) cc_final: 0.8547 (mtm) REVERT: U 196 ASP cc_start: 0.8342 (m-30) cc_final: 0.8067 (m-30) REVERT: U 199 GLU cc_start: 0.8251 (tt0) cc_final: 0.7602 (tp30) REVERT: V 112 ASP cc_start: 0.7944 (m-30) cc_final: 0.6355 (t70) REVERT: V 192 MET cc_start: 0.8905 (mtp) cc_final: 0.8592 (mtm) REVERT: V 238 TYR cc_start: 0.7993 (m-80) cc_final: 0.7681 (m-80) outliers start: 0 outliers final: 0 residues processed: 704 average time/residue: 0.5007 time to fit residues: 518.2717 Evaluate side-chains 459 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 459 time to evaluate : 2.676 ------------------------------------------------------------------------------- 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: 10.0000 chunk 196 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 301 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 224 optimal weight: 0.1980 chunk 349 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS A 259 ASN B 250 HIS C 143 ASN D 62 ASN F 250 HIS F 259 ASN G 45 ASN G 65 ASN G 129 HIS J 65 ASN J 129 HIS K 62 ASN K 65 ASN M 72 GLN M 129 HIS N 45 ASN N 62 ASN N 143 ASN O 250 HIS P 259 ASN Q 65 ASN Q 129 HIS Q 143 ASN R 62 ASN T 169 GLN T 250 HIS T 259 ASN U 65 ASN U 129 HIS U 143 ASN V 62 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30701 Z= 0.188 Angle : 0.542 10.011 41558 Z= 0.281 Chirality : 0.044 0.173 4917 Planarity : 0.004 0.046 5313 Dihedral : 10.066 71.467 4653 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.17 % Allowed : 17.55 % Favored : 79.28 % 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: -2.72 (0.12), residues: 3927 helix: -2.15 (0.12), residues: 1309 sheet: -1.26 (0.17), residues: 814 loop : -1.65 (0.13), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 245 HIS 0.002 0.001 HIS S 250 PHE 0.014 0.001 PHE R 60 TYR 0.010 0.001 TYR A 233 ARG 0.005 0.000 ARG K 55 *********************** 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 614 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 513 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.7702 (OUTLIER) cc_final: 0.7451 (m) REVERT: B 202 ARG cc_start: 0.8350 (mtp180) cc_final: 0.7947 (mtm180) REVERT: C 189 LYS cc_start: 0.7626 (mtpp) cc_final: 0.7338 (mttm) REVERT: D 146 VAL cc_start: 0.7949 (m) cc_final: 0.7738 (p) REVERT: D 167 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6804 (pt0) REVERT: D 168 LYS cc_start: 0.7511 (mtmt) cc_final: 0.7094 (mttp) REVERT: F 233 TYR cc_start: 0.8764 (p90) cc_final: 0.8532 (p90) REVERT: G 93 ASP cc_start: 0.6262 (p0) cc_final: 0.5765 (t0) REVERT: G 253 ARG cc_start: 0.5028 (mtm180) cc_final: 0.3614 (mtt-85) REVERT: J 77 ASP cc_start: 0.7977 (m-30) cc_final: 0.7361 (t0) REVERT: J 132 MET cc_start: 0.6860 (ttm) cc_final: 0.6618 (ttm) REVERT: J 197 ASP cc_start: 0.7470 (m-30) cc_final: 0.7193 (m-30) REVERT: J 231 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7949 (mm110) REVERT: J 238 TYR cc_start: 0.7748 (m-80) cc_final: 0.7415 (m-80) REVERT: K 54 ARG cc_start: 0.7509 (mtt90) cc_final: 0.7072 (mmt180) REVERT: K 176 HIS cc_start: 0.7277 (m-70) cc_final: 0.6737 (m170) REVERT: K 189 LYS cc_start: 0.7309 (mtpp) cc_final: 0.7100 (mttt) REVERT: M 50 MET cc_start: 0.8174 (mmm) cc_final: 0.7937 (mmm) REVERT: M 58 TYR cc_start: 0.8324 (m-80) cc_final: 0.7789 (m-80) REVERT: M 78 LYS cc_start: 0.7739 (pttp) cc_final: 0.7145 (mmtt) REVERT: M 168 LYS cc_start: 0.7133 (ttpp) cc_final: 0.6886 (ttmm) REVERT: N 53 GLU cc_start: 0.8172 (pt0) cc_final: 0.7884 (pt0) REVERT: N 162 LYS cc_start: 0.8014 (mtpt) cc_final: 0.7691 (mttt) REVERT: N 168 LYS cc_start: 0.7919 (mtmt) cc_final: 0.7462 (mtpp) REVERT: N 196 ASP cc_start: 0.8585 (m-30) cc_final: 0.8372 (m-30) REVERT: N 199 GLU cc_start: 0.8234 (tt0) cc_final: 0.7598 (tp30) REVERT: O 161 LYS cc_start: 0.8642 (mtmm) cc_final: 0.8335 (mtpt) REVERT: P 204 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7814 (mtm180) REVERT: Q 3 LYS cc_start: 0.7796 (ttmm) cc_final: 0.7336 (mtmt) REVERT: Q 199 GLU cc_start: 0.8370 (tt0) cc_final: 0.7921 (mt-10) REVERT: Q 206 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7917 (mp) REVERT: R 3 LYS cc_start: 0.8110 (ttmm) cc_final: 0.7815 (tppt) REVERT: R 95 ASP cc_start: 0.7939 (p0) cc_final: 0.7538 (p0) REVERT: R 192 MET cc_start: 0.8938 (mtp) cc_final: 0.8737 (mtm) REVERT: S 158 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7548 (ttpp) REVERT: T 262 ARG cc_start: 0.8264 (tmt-80) cc_final: 0.7967 (tpp80) REVERT: U 77 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7734 (t0) REVERT: U 108 GLU cc_start: 0.7315 (pt0) cc_final: 0.7067 (mp0) REVERT: U 185 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7980 (tt0) REVERT: U 196 ASP cc_start: 0.8337 (m-30) cc_final: 0.8103 (m-30) REVERT: U 199 GLU cc_start: 0.8269 (tt0) cc_final: 0.7733 (tp30) REVERT: V 112 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.6389 (t0) REVERT: V 192 MET cc_start: 0.9006 (mtp) cc_final: 0.8740 (mtm) outliers start: 101 outliers final: 63 residues processed: 589 average time/residue: 0.4580 time to fit residues: 412.4455 Evaluate side-chains 497 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 430 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 233 ASP Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 206 LEU Chi-restraints excluded: chain N residue 233 ASP Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 59 ASP Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 206 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 233 ASP Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 169 GLN Chi-restraints excluded: chain T residue 192 ASP Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 197 ASP Chi-restraints excluded: chain U residue 206 LEU Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 112 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 290 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 350 optimal weight: 0.6980 chunk 378 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 347 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 280 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN E 250 HIS F 259 ASN G 129 HIS H 259 ASN J 84 HIS J 176 HIS K 176 HIS L 259 ASN M 129 HIS M 176 HIS N 45 ASN N 129 HIS N 176 HIS O 259 ASN Q 176 HIS R 176 HIS ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 259 ASN V 129 HIS V 176 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 30701 Z= 0.387 Angle : 0.682 10.028 41558 Z= 0.343 Chirality : 0.048 0.184 4917 Planarity : 0.004 0.043 5313 Dihedral : 9.892 88.973 4653 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.24 % Allowed : 19.06 % Favored : 75.71 % 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: -2.40 (0.12), residues: 3927 helix: -1.69 (0.13), residues: 1320 sheet: -1.12 (0.16), residues: 924 loop : -1.62 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 245 HIS 0.010 0.001 HIS G 129 PHE 0.012 0.002 PHE J 60 TYR 0.018 0.002 TYR O 233 ARG 0.006 0.001 ARG E 262 *********************** 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 617 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 450 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8586 (mtp) cc_final: 0.8363 (mtt) REVERT: A 261 THR cc_start: 0.7681 (OUTLIER) cc_final: 0.7380 (m) REVERT: B 158 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7906 (ttpp) REVERT: B 202 ARG cc_start: 0.8646 (mtp180) cc_final: 0.8434 (mtm-85) REVERT: C 199 GLU cc_start: 0.8045 (tt0) cc_final: 0.7712 (tm-30) REVERT: D 155 MET cc_start: 0.7576 (mmm) cc_final: 0.7372 (mmm) REVERT: E 237 GLU cc_start: 0.8268 (tm-30) cc_final: 0.8024 (tm-30) REVERT: G 93 ASP cc_start: 0.6448 (p0) cc_final: 0.6096 (t0) REVERT: G 233 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6199 (m-30) REVERT: H 177 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8600 (tp) REVERT: J 77 ASP cc_start: 0.8243 (m-30) cc_final: 0.7601 (t0) REVERT: J 206 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8011 (mp) REVERT: J 231 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8043 (mm110) REVERT: J 238 TYR cc_start: 0.7968 (m-80) cc_final: 0.7675 (m-80) REVERT: K 54 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7587 (mtp180) REVERT: K 174 LYS cc_start: 0.7931 (tttt) cc_final: 0.7582 (tppt) REVERT: K 185 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8166 (tt0) REVERT: L 177 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8560 (tp) REVERT: M 78 LYS cc_start: 0.7795 (pttp) cc_final: 0.7143 (mmtt) REVERT: M 104 LYS cc_start: 0.7337 (mtmm) cc_final: 0.6960 (mptt) REVERT: M 238 TYR cc_start: 0.8099 (m-80) cc_final: 0.7778 (m-80) REVERT: N 77 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7568 (t0) REVERT: N 199 GLU cc_start: 0.8450 (tt0) cc_final: 0.7901 (tp30) REVERT: O 161 LYS cc_start: 0.8734 (mtmm) cc_final: 0.8330 (mtpt) REVERT: O 177 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8440 (tp) REVERT: P 204 ARG cc_start: 0.8301 (mtp85) cc_final: 0.7886 (mtm180) REVERT: P 250 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.8088 (t70) REVERT: P 262 ARG cc_start: 0.7976 (tpt90) cc_final: 0.7752 (tpt90) REVERT: Q 3 LYS cc_start: 0.7751 (ttmm) cc_final: 0.7228 (tppt) REVERT: Q 53 GLU cc_start: 0.8215 (pt0) cc_final: 0.8008 (pt0) REVERT: Q 59 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7611 (p0) REVERT: R 3 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7600 (tppt) REVERT: R 106 MET cc_start: 0.7821 (mmm) cc_final: 0.7620 (mmt) REVERT: R 162 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7837 (mtpt) REVERT: T 262 ARG cc_start: 0.8259 (tmt-80) cc_final: 0.8041 (ttp-170) REVERT: U 77 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7891 (t0) REVERT: U 199 GLU cc_start: 0.8479 (tt0) cc_final: 0.7782 (tp30) REVERT: V 192 MET cc_start: 0.8934 (mtp) cc_final: 0.8720 (mtm) outliers start: 167 outliers final: 115 residues processed: 587 average time/residue: 0.4453 time to fit residues: 402.3740 Evaluate side-chains 517 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 392 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 233 ASP Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 233 ASP Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 233 ASP Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain N residue 233 ASP Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 192 ASP Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 250 HIS Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 59 ASP Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 197 ASP Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 176 ASP Chi-restraints excluded: chain S residue 192 ASP Chi-restraints excluded: chain S residue 228 SER Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 250 HIS Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 192 ASP Chi-restraints excluded: chain T residue 228 SER Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 59 ASP Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 72 GLN Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 124 ILE Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 197 ASP Chi-restraints excluded: chain U residue 233 ASP Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 233 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 0.4980 chunk 263 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 351 optimal weight: 4.9990 chunk 372 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 D 84 HIS E 259 ASN G 129 HIS K 72 GLN L 259 ASN M 176 HIS N 45 ASN P 250 HIS Q 72 GLN Q 176 HIS R 176 HIS ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 169 GLN T 259 ASN U 45 ASN ** U 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30701 Z= 0.314 Angle : 0.605 10.011 41558 Z= 0.305 Chirality : 0.046 0.182 4917 Planarity : 0.004 0.044 5313 Dihedral : 9.508 79.784 4653 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.42 % Allowed : 20.91 % Favored : 73.67 % 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: -2.19 (0.12), residues: 3927 helix: -1.42 (0.13), residues: 1320 sheet: -1.04 (0.17), residues: 869 loop : -1.55 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 245 HIS 0.008 0.001 HIS H 250 PHE 0.008 0.001 PHE V 113 TYR 0.019 0.002 TYR A 233 ARG 0.005 0.000 ARG H 202 *********************** 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 588 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 415 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8471 (mtp) cc_final: 0.8208 (mtt) REVERT: A 238 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7688 (p0) REVERT: A 261 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7407 (m) REVERT: B 158 LYS cc_start: 0.8065 (ttmt) cc_final: 0.7782 (ttpp) REVERT: B 177 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8574 (tp) REVERT: C 199 GLU cc_start: 0.8051 (tt0) cc_final: 0.7758 (tm-30) REVERT: D 59 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6462 (p0) REVERT: E 204 ARG cc_start: 0.8368 (mtp85) cc_final: 0.7914 (mtm180) REVERT: G 93 ASP cc_start: 0.6590 (p0) cc_final: 0.6246 (t0) REVERT: G 233 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6227 (m-30) REVERT: J 77 ASP cc_start: 0.8266 (m-30) cc_final: 0.7619 (t0) REVERT: J 206 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8052 (mp) REVERT: K 54 ARG cc_start: 0.7970 (mtt90) cc_final: 0.7381 (mmm-85) REVERT: K 100 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7032 (pm20) REVERT: K 174 LYS cc_start: 0.7865 (tttt) cc_final: 0.7539 (tppt) REVERT: K 185 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8119 (tt0) REVERT: L 177 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8543 (tp) REVERT: M 71 THR cc_start: 0.7668 (OUTLIER) cc_final: 0.7464 (p) REVERT: M 78 LYS cc_start: 0.7626 (pttp) cc_final: 0.7122 (mmtt) REVERT: M 199 GLU cc_start: 0.8706 (tt0) cc_final: 0.8496 (tt0) REVERT: M 238 TYR cc_start: 0.8072 (m-80) cc_final: 0.7813 (m-80) REVERT: N 77 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7703 (t0) REVERT: N 199 GLU cc_start: 0.8459 (tt0) cc_final: 0.7903 (tp30) REVERT: O 158 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7847 (ttpt) REVERT: O 161 LYS cc_start: 0.8773 (mtmm) cc_final: 0.8321 (mtpt) REVERT: P 204 ARG cc_start: 0.8285 (mtp85) cc_final: 0.7896 (mtm180) REVERT: P 262 ARG cc_start: 0.8008 (tpt90) cc_final: 0.7779 (tpt90) REVERT: Q 3 LYS cc_start: 0.7746 (ttmm) cc_final: 0.7243 (tppt) REVERT: Q 53 GLU cc_start: 0.8192 (pt0) cc_final: 0.7969 (pt0) REVERT: Q 59 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7678 (p0) REVERT: R 3 LYS cc_start: 0.8030 (ttmm) cc_final: 0.7576 (tppt) REVERT: R 162 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7867 (mtpt) REVERT: S 177 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8575 (tp) REVERT: T 262 ARG cc_start: 0.8364 (tmt-80) cc_final: 0.8068 (ttp80) REVERT: U 77 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7856 (t0) REVERT: U 199 GLU cc_start: 0.8432 (tt0) cc_final: 0.7941 (tp30) REVERT: V 74 LEU cc_start: 0.8901 (mt) cc_final: 0.8667 (mp) outliers start: 173 outliers final: 120 residues processed: 555 average time/residue: 0.4462 time to fit residues: 382.6193 Evaluate side-chains 526 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 393 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 233 ASP Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 233 ASP Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain M residue 233 ASP Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain N residue 233 ASP Chi-restraints excluded: chain O residue 192 ASP Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 59 ASP Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 72 GLN Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 197 ASP Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 200 GLU Chi-restraints excluded: chain S residue 177 LEU Chi-restraints excluded: chain S residue 192 ASP Chi-restraints excluded: chain S residue 228 SER Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 169 GLN Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 192 ASP Chi-restraints excluded: chain T residue 228 SER Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 197 ASP Chi-restraints excluded: chain U residue 233 ASP Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 233 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 309 optimal weight: 0.4980 chunk 211 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 153 optimal weight: 0.3980 chunk 317 optimal weight: 4.9990 chunk 257 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 chunk 334 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 259 ASN L 259 ASN M 176 HIS N 45 ASN P 250 HIS Q 72 GLN Q 176 HIS R 176 HIS R 222 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 259 ASN U 72 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30701 Z= 0.211 Angle : 0.527 8.177 41558 Z= 0.269 Chirality : 0.044 0.170 4917 Planarity : 0.003 0.045 5313 Dihedral : 9.172 77.477 4653 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.05 % Allowed : 22.57 % Favored : 72.38 % 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: -1.84 (0.13), residues: 3927 helix: -1.05 (0.14), residues: 1320 sheet: -0.84 (0.17), residues: 869 loop : -1.42 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 245 HIS 0.008 0.001 HIS H 250 PHE 0.008 0.001 PHE Q 113 TYR 0.021 0.001 TYR O 233 ARG 0.005 0.000 ARG H 202 *********************** 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 593 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 432 time to evaluate : 3.251 Fit side-chains revert: symmetry clash REVERT: A 168 MET cc_start: 0.8498 (mtp) cc_final: 0.8241 (mtt) REVERT: A 238 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7692 (p0) REVERT: A 261 THR cc_start: 0.7669 (OUTLIER) cc_final: 0.7391 (m) REVERT: B 158 LYS cc_start: 0.8036 (ttmt) cc_final: 0.7788 (ttpp) REVERT: C 199 GLU cc_start: 0.8062 (tt0) cc_final: 0.7778 (tm-30) REVERT: C 254 PHE cc_start: 0.7459 (m-80) cc_final: 0.7183 (m-80) REVERT: E 204 ARG cc_start: 0.8329 (mtp85) cc_final: 0.7866 (mtm180) REVERT: G 93 ASP cc_start: 0.6491 (p0) cc_final: 0.6206 (t0) REVERT: H 168 MET cc_start: 0.8749 (mtp) cc_final: 0.8546 (mtp) REVERT: H 177 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8662 (tp) REVERT: J 77 ASP cc_start: 0.8084 (m-30) cc_final: 0.7496 (t0) REVERT: J 185 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7582 (tt0) REVERT: J 206 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8042 (mp) REVERT: K 54 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7428 (mmm-85) REVERT: K 77 ASP cc_start: 0.8160 (m-30) cc_final: 0.7899 (m-30) REVERT: K 100 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7125 (mm-30) REVERT: K 174 LYS cc_start: 0.7784 (tttt) cc_final: 0.7460 (tppt) REVERT: K 185 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8057 (tt0) REVERT: K 199 GLU cc_start: 0.7906 (tt0) cc_final: 0.7620 (tm-30) REVERT: L 177 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8518 (tp) REVERT: M 78 LYS cc_start: 0.7644 (pttp) cc_final: 0.7151 (mmtt) REVERT: M 238 TYR cc_start: 0.8057 (m-80) cc_final: 0.7714 (m-80) REVERT: N 199 GLU cc_start: 0.8438 (tt0) cc_final: 0.7897 (tp30) REVERT: O 161 LYS cc_start: 0.8711 (mtmm) cc_final: 0.8280 (mtpt) REVERT: P 204 ARG cc_start: 0.8324 (mtp85) cc_final: 0.7856 (mtm180) REVERT: P 262 ARG cc_start: 0.7982 (tpt90) cc_final: 0.7757 (tpt90) REVERT: Q 3 LYS cc_start: 0.7726 (ttmm) cc_final: 0.7268 (tppt) REVERT: Q 53 GLU cc_start: 0.8159 (pt0) cc_final: 0.7955 (pt0) REVERT: Q 59 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7707 (p0) REVERT: Q 60 PHE cc_start: 0.8507 (t80) cc_final: 0.8298 (t80) REVERT: R 3 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7589 (tppt) REVERT: R 59 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7979 (p0) REVERT: R 162 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7804 (mmtm) REVERT: T 262 ARG cc_start: 0.8373 (tmt-80) cc_final: 0.8058 (tpp80) REVERT: U 199 GLU cc_start: 0.8368 (tt0) cc_final: 0.7865 (tp30) REVERT: V 74 LEU cc_start: 0.8850 (mt) cc_final: 0.8619 (mp) REVERT: V 80 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8119 (mp) outliers start: 161 outliers final: 123 residues processed: 557 average time/residue: 0.4458 time to fit residues: 384.7691 Evaluate side-chains 539 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 407 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 233 ASP Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 117 ILE Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 233 ASP Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain N residue 233 ASP Chi-restraints excluded: chain O residue 192 ASP Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 59 ASP Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 176 ASP Chi-restraints excluded: chain S residue 192 ASP Chi-restraints excluded: chain S residue 228 SER Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 192 ASP Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 59 ASP Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 72 GLN Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 148 SER Chi-restraints excluded: chain U residue 197 ASP Chi-restraints excluded: chain U residue 233 ASP Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 80 LEU Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 179 LEU Chi-restraints excluded: chain V residue 181 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 9.9990 chunk 335 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 218 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 372 optimal weight: 0.9980 chunk 309 optimal weight: 1.9990 chunk 172 optimal weight: 0.0670 chunk 30 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN E 259 ASN M 176 HIS Q 72 GLN R 176 HIS ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 72 GLN V 176 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30701 Z= 0.247 Angle : 0.552 8.737 41558 Z= 0.279 Chirality : 0.044 0.167 4917 Planarity : 0.003 0.046 5313 Dihedral : 9.147 80.480 4653 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.67 % Allowed : 22.07 % Favored : 72.26 % 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: -1.69 (0.13), residues: 3927 helix: -0.90 (0.14), residues: 1320 sheet: -0.76 (0.17), residues: 869 loop : -1.36 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 245 HIS 0.009 0.001 HIS F 250 PHE 0.008 0.001 PHE R 113 TYR 0.021 0.001 TYR O 233 ARG 0.005 0.000 ARG L 216 *********************** 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 582 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 401 time to evaluate : 3.470 Fit side-chains REVERT: A 168 MET cc_start: 0.8490 (mtp) cc_final: 0.8262 (mtt) REVERT: A 261 THR cc_start: 0.7689 (OUTLIER) cc_final: 0.7435 (m) REVERT: B 158 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7759 (ttpp) REVERT: B 177 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8530 (tp) REVERT: C 167 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7520 (pt0) REVERT: C 199 GLU cc_start: 0.8091 (tt0) cc_final: 0.7798 (tm-30) REVERT: D 59 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6405 (p0) REVERT: H 177 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8652 (tp) REVERT: H 250 HIS cc_start: 0.7531 (t-170) cc_final: 0.7255 (t-170) REVERT: J 77 ASP cc_start: 0.8227 (m-30) cc_final: 0.7571 (t0) REVERT: J 185 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7590 (tt0) REVERT: J 206 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8072 (mp) REVERT: K 54 ARG cc_start: 0.7974 (mtt90) cc_final: 0.7422 (mmm-85) REVERT: K 174 LYS cc_start: 0.7799 (tttt) cc_final: 0.7495 (tppt) REVERT: K 199 GLU cc_start: 0.7972 (tt0) cc_final: 0.7680 (tm-30) REVERT: L 177 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8544 (tp) REVERT: M 78 LYS cc_start: 0.7635 (pttp) cc_final: 0.7139 (mmtt) REVERT: M 80 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7920 (mp) REVERT: M 238 TYR cc_start: 0.8041 (m-80) cc_final: 0.7669 (m-80) REVERT: N 199 GLU cc_start: 0.8448 (tt0) cc_final: 0.7901 (tp30) REVERT: O 161 LYS cc_start: 0.8767 (mtmm) cc_final: 0.8306 (mtpt) REVERT: P 204 ARG cc_start: 0.8343 (mtp85) cc_final: 0.7862 (mtm180) REVERT: P 262 ARG cc_start: 0.7986 (tpt90) cc_final: 0.7754 (tpt90) REVERT: Q 3 LYS cc_start: 0.7726 (ttmm) cc_final: 0.7252 (tppt) REVERT: Q 59 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7693 (p0) REVERT: R 3 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7559 (tppt) REVERT: R 59 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7991 (p0) REVERT: R 95 ASP cc_start: 0.7837 (p0) cc_final: 0.7589 (p0) REVERT: R 162 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7777 (mmtm) REVERT: T 262 ARG cc_start: 0.8373 (tmt-80) cc_final: 0.8069 (tpp80) REVERT: U 199 GLU cc_start: 0.8353 (tt0) cc_final: 0.7886 (tp30) REVERT: V 74 LEU cc_start: 0.8879 (mt) cc_final: 0.8638 (mp) REVERT: V 80 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8094 (mp) outliers start: 181 outliers final: 144 residues processed: 541 average time/residue: 0.4581 time to fit residues: 382.6952 Evaluate side-chains 545 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 391 time to evaluate : 3.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 233 ASP Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 233 ASP Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain N residue 233 ASP Chi-restraints excluded: chain O residue 192 ASP Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 59 ASP Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 72 GLN Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 197 ASP Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 200 GLU Chi-restraints excluded: chain S residue 176 ASP Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 192 ASP Chi-restraints excluded: chain S residue 228 SER Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 192 ASP Chi-restraints excluded: chain T residue 228 SER Chi-restraints excluded: chain T residue 242 SER Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 72 GLN Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 148 SER Chi-restraints excluded: chain U residue 197 ASP Chi-restraints excluded: chain U residue 233 ASP Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 80 LEU Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 179 LEU Chi-restraints excluded: chain V residue 181 ARG Chi-restraints excluded: chain V residue 233 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 212 optimal weight: 0.0970 chunk 272 optimal weight: 0.5980 chunk 210 optimal weight: 0.9980 chunk 313 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 371 optimal weight: 4.9990 chunk 232 optimal weight: 0.9990 chunk 226 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN C 65 ASN C 222 GLN E 259 ASN ** N 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN R 176 HIS S 250 HIS ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 72 GLN V 176 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30701 Z= 0.147 Angle : 0.484 7.113 41558 Z= 0.249 Chirality : 0.042 0.157 4917 Planarity : 0.003 0.047 5313 Dihedral : 8.851 86.353 4653 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.11 % Allowed : 24.14 % Favored : 71.76 % 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: -1.47 (0.13), residues: 3927 helix: -0.55 (0.14), residues: 1320 sheet: -0.76 (0.16), residues: 1034 loop : -1.33 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP I 245 HIS 0.008 0.001 HIS T 250 PHE 0.007 0.001 PHE Q 113 TYR 0.020 0.001 TYR O 233 ARG 0.003 0.000 ARG H 202 *********************** 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 536 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 405 time to evaluate : 3.427 Fit side-chains REVERT: A 168 MET cc_start: 0.8467 (mtp) cc_final: 0.8226 (mtt) REVERT: A 261 THR cc_start: 0.7626 (OUTLIER) cc_final: 0.7363 (m) REVERT: B 158 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7781 (ttpp) REVERT: C 167 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7472 (pt0) REVERT: C 199 GLU cc_start: 0.8099 (tt0) cc_final: 0.7815 (tm-30) REVERT: C 254 PHE cc_start: 0.7432 (m-80) cc_final: 0.7183 (m-80) REVERT: D 206 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7926 (mp) REVERT: E 204 ARG cc_start: 0.8376 (mtp85) cc_final: 0.7814 (mtm180) REVERT: H 177 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8614 (tp) REVERT: J 77 ASP cc_start: 0.8197 (m-30) cc_final: 0.7552 (t0) REVERT: J 185 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7542 (tt0) REVERT: J 206 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8006 (mp) REVERT: K 77 ASP cc_start: 0.8123 (m-30) cc_final: 0.7858 (m-30) REVERT: K 174 LYS cc_start: 0.7718 (tttt) cc_final: 0.7425 (tppt) REVERT: K 176 HIS cc_start: 0.8067 (m90) cc_final: 0.7605 (m170) REVERT: K 199 GLU cc_start: 0.7919 (tt0) cc_final: 0.7648 (tm-30) REVERT: L 177 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8475 (tp) REVERT: M 78 LYS cc_start: 0.7643 (pttp) cc_final: 0.7147 (mmtt) REVERT: M 238 TYR cc_start: 0.7949 (m-80) cc_final: 0.7627 (m-80) REVERT: N 199 GLU cc_start: 0.8402 (tt0) cc_final: 0.8044 (tp30) REVERT: O 161 LYS cc_start: 0.8738 (mtmm) cc_final: 0.8290 (mtpt) REVERT: P 204 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7834 (mtm180) REVERT: P 262 ARG cc_start: 0.7953 (tpt90) cc_final: 0.7705 (tpt90) REVERT: Q 3 LYS cc_start: 0.7745 (ttmm) cc_final: 0.7283 (tppt) REVERT: Q 59 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7586 (p0) REVERT: Q 112 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.6353 (t0) REVERT: R 3 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7627 (tppt) REVERT: R 59 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8127 (p0) REVERT: R 162 LYS cc_start: 0.8236 (mtpt) cc_final: 0.7788 (mmtm) REVERT: T 262 ARG cc_start: 0.8329 (tmt-80) cc_final: 0.8065 (tpp80) REVERT: U 162 LYS cc_start: 0.7967 (mtpt) cc_final: 0.7584 (mmmt) REVERT: U 199 GLU cc_start: 0.8301 (tt0) cc_final: 0.7826 (tp30) REVERT: U 200 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: V 80 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8047 (mp) REVERT: V 95 ASP cc_start: 0.8186 (p0) cc_final: 0.7367 (t70) REVERT: V 240 ASP cc_start: 0.8062 (m-30) cc_final: 0.7813 (m-30) outliers start: 131 outliers final: 102 residues processed: 500 average time/residue: 0.4369 time to fit residues: 338.5723 Evaluate side-chains 495 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 383 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 233 ASP Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 233 ASP Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain N residue 233 ASP Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 59 ASP Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 200 GLU Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain S residue 192 ASP Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 192 ASP Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 197 ASP Chi-restraints excluded: chain U residue 200 GLU Chi-restraints excluded: chain U residue 233 ASP Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 80 LEU Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 179 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 252 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 291 optimal weight: 0.4980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 GLN E 259 ASN H 259 ASN I 221 GLN K 176 HIS M 176 HIS Q 72 GLN Q 84 HIS ** R 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30701 Z= 0.280 Angle : 0.572 8.969 41558 Z= 0.288 Chirality : 0.045 0.163 4917 Planarity : 0.004 0.048 5313 Dihedral : 9.103 89.250 4653 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.02 % Allowed : 23.45 % Favored : 71.54 % 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: -1.49 (0.13), residues: 3927 helix: -0.62 (0.14), residues: 1320 sheet: -0.78 (0.16), residues: 1023 loop : -1.27 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 245 HIS 0.010 0.001 HIS B 250 PHE 0.009 0.001 PHE U 254 TYR 0.020 0.002 TYR O 233 ARG 0.004 0.000 ARG R 181 *********************** 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 553 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 393 time to evaluate : 3.267 Fit side-chains REVERT: A 168 MET cc_start: 0.8491 (mtp) cc_final: 0.8241 (mtt) REVERT: A 261 THR cc_start: 0.7685 (OUTLIER) cc_final: 0.7405 (m) REVERT: B 158 LYS cc_start: 0.8049 (ttmt) cc_final: 0.7808 (ttpp) REVERT: C 167 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7560 (pt0) REVERT: C 199 GLU cc_start: 0.8065 (tt0) cc_final: 0.7825 (tm-30) REVERT: D 206 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8010 (mp) REVERT: H 177 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8645 (tp) REVERT: J 59 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6454 (p0) REVERT: J 77 ASP cc_start: 0.8162 (m-30) cc_final: 0.7518 (t0) REVERT: J 185 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7590 (tt0) REVERT: J 206 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8077 (mp) REVERT: K 174 LYS cc_start: 0.7792 (tttt) cc_final: 0.7496 (tppt) REVERT: K 176 HIS cc_start: 0.7957 (m-70) cc_final: 0.7474 (m170) REVERT: K 199 GLU cc_start: 0.7970 (tt0) cc_final: 0.7716 (tm-30) REVERT: L 177 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8548 (tp) REVERT: M 238 TYR cc_start: 0.8037 (m-80) cc_final: 0.7619 (m-80) REVERT: N 199 GLU cc_start: 0.8427 (tt0) cc_final: 0.8171 (tp30) REVERT: O 161 LYS cc_start: 0.8728 (mtmm) cc_final: 0.8276 (mtpt) REVERT: P 262 ARG cc_start: 0.8010 (tpt90) cc_final: 0.7738 (tpt90) REVERT: Q 3 LYS cc_start: 0.7732 (ttmm) cc_final: 0.7226 (tppt) REVERT: Q 59 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7664 (p0) REVERT: R 3 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7557 (tppt) REVERT: R 43 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7808 (mt) REVERT: R 59 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8122 (p0) REVERT: R 162 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7748 (mmtm) REVERT: T 262 ARG cc_start: 0.8326 (tmt-80) cc_final: 0.8084 (tpp80) REVERT: U 199 GLU cc_start: 0.8315 (tt0) cc_final: 0.7892 (tp30) REVERT: V 50 MET cc_start: 0.8123 (mmm) cc_final: 0.7716 (mmm) REVERT: V 80 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8075 (mp) REVERT: V 95 ASP cc_start: 0.8229 (p0) cc_final: 0.7363 (t70) outliers start: 160 outliers final: 128 residues processed: 520 average time/residue: 0.4354 time to fit residues: 350.6201 Evaluate side-chains 518 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 380 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 233 ASP Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 117 ILE Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 233 ASP Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain N residue 233 ASP Chi-restraints excluded: chain O residue 176 ASP Chi-restraints excluded: chain O residue 192 ASP Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 59 ASP Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 197 ASP Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 72 GLN Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 200 GLU Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 192 ASP Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 250 HIS Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 192 ASP Chi-restraints excluded: chain T residue 228 SER Chi-restraints excluded: chain T residue 242 SER Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 197 ASP Chi-restraints excluded: chain U residue 233 ASP Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 80 LEU Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 179 LEU Chi-restraints excluded: chain V residue 181 ARG Chi-restraints excluded: chain V residue 233 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 0.7980 chunk 355 optimal weight: 0.0770 chunk 324 optimal weight: 6.9990 chunk 345 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 271 optimal weight: 0.0470 chunk 106 optimal weight: 30.0000 chunk 312 optimal weight: 0.0870 chunk 327 optimal weight: 6.9990 chunk 344 optimal weight: 2.9990 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 GLN E 259 ASN G 84 HIS ** H 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN M 176 HIS ** N 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN R 176 HIS T 259 ASN ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 72 GLN V 176 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 30701 Z= 0.153 Angle : 0.489 6.919 41558 Z= 0.250 Chirality : 0.043 0.158 4917 Planarity : 0.003 0.049 5313 Dihedral : 8.778 81.744 4653 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.98 % Allowed : 24.83 % Favored : 71.19 % 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: -0.26 (0.14), residues: 1309 sheet: -0.66 (0.16), residues: 1034 loop : -1.28 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP I 245 HIS 0.008 0.001 HIS T 250 PHE 0.007 0.001 PHE G 113 TYR 0.020 0.001 TYR O 233 ARG 0.004 0.000 ARG A 262 *********************** 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 523 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 396 time to evaluate : 3.412 Fit side-chains REVERT: A 168 MET cc_start: 0.8461 (mtp) cc_final: 0.8225 (mtt) REVERT: A 261 THR cc_start: 0.7508 (OUTLIER) cc_final: 0.7219 (m) REVERT: B 158 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7741 (ttpp) REVERT: C 167 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7572 (pt0) REVERT: C 199 GLU cc_start: 0.8063 (tt0) cc_final: 0.7821 (tm-30) REVERT: D 206 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7896 (mp) REVERT: E 204 ARG cc_start: 0.8370 (mtp85) cc_final: 0.7816 (mtm180) REVERT: H 177 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8620 (tp) REVERT: J 185 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7559 (tt0) REVERT: J 206 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8015 (mp) REVERT: K 174 LYS cc_start: 0.7735 (tttt) cc_final: 0.7463 (tppt) REVERT: K 176 HIS cc_start: 0.7923 (m-70) cc_final: 0.7487 (m170) REVERT: K 248 LYS cc_start: 0.7225 (mttp) cc_final: 0.6826 (mtpt) REVERT: L 177 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8482 (tp) REVERT: N 199 GLU cc_start: 0.8392 (tt0) cc_final: 0.8134 (tp30) REVERT: O 161 LYS cc_start: 0.8669 (mtmm) cc_final: 0.8240 (mtpt) REVERT: P 204 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7834 (mtm180) REVERT: P 262 ARG cc_start: 0.7989 (tpt90) cc_final: 0.7666 (tpt90) REVERT: Q 3 LYS cc_start: 0.7742 (ttmm) cc_final: 0.7280 (tppt) REVERT: Q 59 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7576 (p0) REVERT: Q 112 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.6361 (t0) REVERT: R 3 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7607 (tppt) REVERT: R 59 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8189 (p0) REVERT: R 72 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7865 (pt0) REVERT: R 162 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7796 (mmtm) REVERT: T 262 ARG cc_start: 0.8324 (tmt-80) cc_final: 0.8089 (tpp80) REVERT: U 199 GLU cc_start: 0.8234 (tt0) cc_final: 0.8017 (tp30) REVERT: V 50 MET cc_start: 0.8056 (mmm) cc_final: 0.7706 (mmm) REVERT: V 80 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8044 (mp) REVERT: V 95 ASP cc_start: 0.8204 (p0) cc_final: 0.7383 (t70) REVERT: V 112 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.6264 (t0) REVERT: V 240 ASP cc_start: 0.8057 (m-30) cc_final: 0.7812 (m-30) outliers start: 127 outliers final: 109 residues processed: 490 average time/residue: 0.4500 time to fit residues: 340.9493 Evaluate side-chains 496 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 376 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 233 ASP Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain N residue 233 ASP Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 59 ASP Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 197 ASP Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 72 GLN Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 200 GLU Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 192 ASP Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 192 ASP Chi-restraints excluded: chain T residue 228 SER Chi-restraints excluded: chain T residue 242 SER Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 72 GLN Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 233 ASP Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 80 LEU Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 181 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 0.2980 chunk 365 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 254 optimal weight: 8.9990 chunk 383 optimal weight: 5.9990 chunk 353 optimal weight: 4.9990 chunk 305 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 235 optimal weight: 0.6980 chunk 187 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 GLN E 259 ASN G 222 GLN ** H 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN M 176 HIS R 176 HIS T 259 ASN ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 72 GLN V 176 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30701 Z= 0.241 Angle : 0.549 8.569 41558 Z= 0.276 Chirality : 0.045 0.163 4917 Planarity : 0.003 0.050 5313 Dihedral : 8.950 78.485 4653 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.29 % Allowed : 24.45 % Favored : 71.25 % 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: -1.27 (0.13), residues: 3927 helix: -0.28 (0.14), residues: 1309 sheet: -0.72 (0.16), residues: 1034 loop : -1.25 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 245 HIS 0.010 0.001 HIS B 250 PHE 0.018 0.001 PHE C 254 TYR 0.020 0.001 TYR A 233 ARG 0.005 0.000 ARG K 154 ********************** 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 522 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 385 time to evaluate : 3.421 Fit side-chains REVERT: A 168 MET cc_start: 0.8486 (mtp) cc_final: 0.8189 (mtt) REVERT: A 261 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7387 (m) REVERT: B 158 LYS cc_start: 0.7997 (ttmt) cc_final: 0.7766 (ttpp) REVERT: C 167 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7627 (pt0) REVERT: C 199 GLU cc_start: 0.8131 (tt0) cc_final: 0.7892 (tm-30) REVERT: D 206 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7960 (mp) REVERT: H 177 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8615 (tp) REVERT: J 59 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.6388 (p0) REVERT: J 185 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7579 (tt0) REVERT: J 206 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8074 (mp) REVERT: K 77 ASP cc_start: 0.8230 (m-30) cc_final: 0.7874 (m-30) REVERT: K 174 LYS cc_start: 0.7771 (tttt) cc_final: 0.7472 (tppt) REVERT: K 176 HIS cc_start: 0.7947 (m-70) cc_final: 0.7497 (m170) REVERT: L 177 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8516 (tp) REVERT: N 199 GLU cc_start: 0.8416 (tt0) cc_final: 0.8163 (tp30) REVERT: O 161 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8251 (mtpt) REVERT: P 262 ARG cc_start: 0.7973 (tpt90) cc_final: 0.7639 (tpt90) REVERT: Q 3 LYS cc_start: 0.7722 (ttmm) cc_final: 0.7229 (tppt) REVERT: Q 59 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7647 (p0) REVERT: R 3 LYS cc_start: 0.8018 (ttmm) cc_final: 0.7521 (tppt) REVERT: R 59 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8100 (p0) REVERT: R 72 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7904 (pt0) REVERT: R 162 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7784 (mmtm) REVERT: T 262 ARG cc_start: 0.8334 (tmt-80) cc_final: 0.8115 (tpp80) REVERT: U 162 LYS cc_start: 0.7744 (mtpt) cc_final: 0.7353 (mttt) REVERT: U 199 GLU cc_start: 0.8337 (tt0) cc_final: 0.8057 (tp30) REVERT: V 50 MET cc_start: 0.8057 (mmm) cc_final: 0.7678 (mmm) REVERT: V 80 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8115 (mp) REVERT: V 95 ASP cc_start: 0.8228 (p0) cc_final: 0.7371 (t70) outliers start: 137 outliers final: 119 residues processed: 490 average time/residue: 0.4453 time to fit residues: 339.3275 Evaluate side-chains 512 residues out of total 3190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 383 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 233 ASP Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 ASP Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 117 ILE Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 233 ASP Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain N residue 233 ASP Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 59 ASP Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 197 ASP Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 72 GLN Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 200 GLU Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 192 ASP Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 192 ASP Chi-restraints excluded: chain T residue 228 SER Chi-restraints excluded: chain T residue 242 SER Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 59 ASP Chi-restraints excluded: chain U residue 72 GLN Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 197 ASP Chi-restraints excluded: chain U residue 233 ASP Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 80 LEU Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 181 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 242 optimal weight: 3.9990 chunk 325 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 281 optimal weight: 0.0270 chunk 45 optimal weight: 4.9990 chunk 84 optimal weight: 0.0060 chunk 305 optimal weight: 0.6980 chunk 128 optimal weight: 9.9990 chunk 314 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.8656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN C 176 HIS C 222 GLN E 259 ASN ** H 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 259 ASN K 222 GLN M 176 HIS ** N 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 HIS T 259 ASN ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 72 GLN ** U 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 176 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.155406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.124816 restraints weight = 34261.215| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.88 r_work: 0.3176 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30701 Z= 0.181 Angle : 0.510 7.896 41558 Z= 0.258 Chirality : 0.043 0.160 4917 Planarity : 0.003 0.050 5313 Dihedral : 8.806 74.325 4653 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.29 % Allowed : 24.61 % Favored : 71.10 % 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: -1.16 (0.13), residues: 3927 helix: -0.15 (0.14), residues: 1309 sheet: -0.64 (0.16), residues: 1034 loop : -1.23 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 245 HIS 0.008 0.001 HIS F 250 PHE 0.021 0.001 PHE C 254 TYR 0.020 0.001 TYR O 233 ARG 0.005 0.000 ARG K 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8044.93 seconds wall clock time: 144 minutes 58.94 seconds (8698.94 seconds total)