Starting phenix.real_space_refine on Fri Mar 22 14:04:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlq_11272/03_2024/6zlq_11272.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlq_11272/03_2024/6zlq_11272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlq_11272/03_2024/6zlq_11272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlq_11272/03_2024/6zlq_11272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlq_11272/03_2024/6zlq_11272.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlq_11272/03_2024/6zlq_11272.pdb" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 16 7.16 5 S 96 5.16 5 C 21156 2.51 5 N 6081 2.21 5 O 6474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Z GLU 12": "OE1" <-> "OE2" Residue "Z ARG 40": "NH1" <-> "NH2" Residue "Z ARG 53": "NH1" <-> "NH2" Residue "Z GLU 57": "OE1" <-> "OE2" Residue "Z PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 88": "OD1" <-> "OD2" Residue "Z GLU 89": "OE1" <-> "OE2" Residue "Z ASP 113": "OD1" <-> "OD2" Residue "Z ARG 121": "NH1" <-> "NH2" Residue "Z ASP 128": "OD1" <-> "OD2" Residue "Z TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 185": "OD1" <-> "OD2" Residue "A GLU 12": "OE1" <-> "OE2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ASP 128": "OD1" <-> "OD2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "C ARG 40": "NH1" <-> "NH2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ASP 42": "OD1" <-> "OD2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E ASP 113": "OD1" <-> "OD2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G ARG 40": "NH1" <-> "NH2" Residue "G ASP 41": "OD1" <-> "OD2" Residue "G ASP 42": "OD1" <-> "OD2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G ASP 113": "OD1" <-> "OD2" Residue "G ARG 121": "NH1" <-> "NH2" Residue "G GLU 131": "OE1" <-> "OE2" Residue "G TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 185": "OD1" <-> "OD2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "H ASP 42": "OD1" <-> "OD2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H ARG 60": "NH1" <-> "NH2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 183": "OD1" <-> "OD2" Residue "I GLU 12": "OE1" <-> "OE2" Residue "I ARG 40": "NH1" <-> "NH2" Residue "I ASP 42": "OD1" <-> "OD2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I GLU 58": "OE1" <-> "OE2" Residue "I PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 98": "OE1" <-> "OE2" Residue "I ASP 128": "OD1" <-> "OD2" Residue "I GLU 131": "OE1" <-> "OE2" Residue "I TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 12": "OE1" <-> "OE2" Residue "J ARG 40": "NH1" <-> "NH2" Residue "J ASP 42": "OD1" <-> "OD2" Residue "J ARG 60": "NH1" <-> "NH2" Residue "J ASP 72": "OD1" <-> "OD2" Residue "J PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "J TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 40": "NH1" <-> "NH2" Residue "K ASP 41": "OD1" <-> "OD2" Residue "K ASP 42": "OD1" <-> "OD2" Residue "K GLU 54": "OE1" <-> "OE2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K GLU 131": "OE1" <-> "OE2" Residue "K TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 185": "OD1" <-> "OD2" Residue "L GLU 12": "OE1" <-> "OE2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "L ASP 42": "OD1" <-> "OD2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 76": "NH1" <-> "NH2" Residue "L PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 88": "OD1" <-> "OD2" Residue "L TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 185": "OD1" <-> "OD2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ASP 41": "OD1" <-> "OD2" Residue "M ASP 42": "OD1" <-> "OD2" Residue "M GLU 54": "OE1" <-> "OE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M GLU 64": "OE1" <-> "OE2" Residue "M GLU 68": "OE1" <-> "OE2" Residue "M PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 131": "OE1" <-> "OE2" Residue "M TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 183": "OD1" <-> "OD2" Residue "M ASP 185": "OD1" <-> "OD2" Residue "N GLU 12": "OE1" <-> "OE2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ASP 42": "OD1" <-> "OD2" Residue "N GLU 58": "OE1" <-> "OE2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 88": "OD1" <-> "OD2" Residue "N ASP 128": "OD1" <-> "OD2" Residue "N TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 185": "OD1" <-> "OD2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O ARG 40": "NH1" <-> "NH2" Residue "O ASP 42": "OD1" <-> "OD2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "O GLU 61": "OE1" <-> "OE2" Residue "O ASP 72": "OD1" <-> "OD2" Residue "O PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 88": "OD1" <-> "OD2" Residue "O TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 185": "OD1" <-> "OD2" Residue "P GLU 12": "OE1" <-> "OE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ASP 41": "OD1" <-> "OD2" Residue "P ASP 42": "OD1" <-> "OD2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P GLU 68": "OE1" <-> "OE2" Residue "P ARG 76": "NH1" <-> "NH2" Residue "P PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 131": "OE1" <-> "OE2" Residue "P TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 185": "OD1" <-> "OD2" Residue "Q GLU 12": "OE1" <-> "OE2" Residue "Q TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 40": "NH1" <-> "NH2" Residue "Q ASP 42": "OD1" <-> "OD2" Residue "Q ARG 60": "NH1" <-> "NH2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q ASP 72": "OD1" <-> "OD2" Residue "Q PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 128": "OD1" <-> "OD2" Residue "Q TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 183": "OD1" <-> "OD2" Residue "Q ASP 185": "OD1" <-> "OD2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R ARG 40": "NH1" <-> "NH2" Residue "R ASP 42": "OD1" <-> "OD2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R GLU 61": "OE1" <-> "OE2" Residue "R GLU 64": "OE1" <-> "OE2" Residue "R ASP 72": "OD1" <-> "OD2" Residue "R PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 89": "OE1" <-> "OE2" Residue "R GLU 104": "OE1" <-> "OE2" Residue "R TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 185": "OD1" <-> "OD2" Residue "S GLU 12": "OE1" <-> "OE2" Residue "S ARG 40": "NH1" <-> "NH2" Residue "S ASP 42": "OD1" <-> "OD2" Residue "S ARG 60": "NH1" <-> "NH2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S GLU 68": "OE1" <-> "OE2" Residue "S ASP 72": "OD1" <-> "OD2" Residue "S PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 88": "OD1" <-> "OD2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S GLU 104": "OE1" <-> "OE2" Residue "S TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 185": "OD1" <-> "OD2" Residue "T GLU 12": "OE1" <-> "OE2" Residue "T ASP 39": "OD1" <-> "OD2" Residue "T ARG 40": "NH1" <-> "NH2" Residue "T ASP 42": "OD1" <-> "OD2" Residue "T ARG 60": "NH1" <-> "NH2" Residue "T ASP 72": "OD1" <-> "OD2" Residue "T PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 138": "OE1" <-> "OE2" Residue "U ARG 40": "NH1" <-> "NH2" Residue "U ASP 41": "OD1" <-> "OD2" Residue "U ASP 42": "OD1" <-> "OD2" Residue "U GLU 54": "OE1" <-> "OE2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U ARG 60": "NH1" <-> "NH2" Residue "U GLU 64": "OE1" <-> "OE2" Residue "U GLU 68": "OE1" <-> "OE2" Residue "U PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 128": "OD1" <-> "OD2" Residue "U GLU 131": "OE1" <-> "OE2" Residue "U TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 185": "OD1" <-> "OD2" Residue "V GLU 12": "OE1" <-> "OE2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "V ASP 42": "OD1" <-> "OD2" Residue "V GLU 54": "OE1" <-> "OE2" Residue "V PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 95": "OE1" <-> "OE2" Residue "V ASP 128": "OD1" <-> "OD2" Residue "V TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 183": "OD1" <-> "OD2" Residue "V ASP 185": "OD1" <-> "OD2" Residue "W ARG 40": "NH1" <-> "NH2" Residue "W ASP 41": "OD1" <-> "OD2" Residue "W ASP 42": "OD1" <-> "OD2" Residue "W GLU 64": "OE1" <-> "OE2" Residue "W PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 95": "OE1" <-> "OE2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "W TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 185": "OD1" <-> "OD2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B ASP 42": "OD1" <-> "OD2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B ASP 128": "OD1" <-> "OD2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 185": "OD1" <-> "OD2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 185": "OD1" <-> "OD2" Residue "F GLU 12": "OE1" <-> "OE2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ASP 41": "OD1" <-> "OD2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F GLU 54": "OE1" <-> "OE2" Residue "F GLU 68": "OE1" <-> "OE2" Residue "F PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F ASP 113": "OD1" <-> "OD2" Residue "F ASP 128": "OD1" <-> "OD2" Residue "F TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 185": "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: 33823 Number of models: 1 Model: "" Number of chains: 38 Chain: "Z" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "A" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "C" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "E" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "G" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "H" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "I" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "J" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "K" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "L" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "M" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "N" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "O" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "P" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "Q" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "R" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "S" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "T" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "U" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "V" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "W" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "B" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "D" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "F" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6624 SG CYS G 127 94.590 35.355 94.952 1.00 49.43 S ATOM 3812 SG CYS C 127 32.999 92.115 94.710 1.00 51.15 S ATOM 33401 SG CYS F 127 34.999 96.220 93.578 1.00 51.16 S ATOM 8037 SG CYS H 127 92.337 32.586 30.226 1.00 49.75 S ATOM 22132 SG CYS R 127 95.960 35.310 31.733 1.00 49.70 S ATOM 29176 SG CYS W 127 94.868 31.421 34.162 1.00 49.03 S ATOM 9450 SG CYS I 127 35.297 94.965 30.333 1.00 48.26 S ATOM 24944 SG CYS T 127 31.599 92.306 31.715 1.00 47.82 S ATOM 15081 SG CYS M 127 32.683 96.197 34.174 1.00 48.96 S ATOM 24944 SG CYS T 127 31.599 92.306 31.715 1.00 47.82 S ATOM 10856 SG CYS J 127 92.271 95.991 31.720 1.00 48.41 S ATOM 20726 SG CYS Q 127 94.996 92.349 30.226 1.00 48.38 S ATOM 30589 SG CYS B 127 96.337 92.604 93.409 1.00 50.22 S ATOM 19313 SG CYS P 127 96.110 94.896 34.196 1.00 48.70 S ATOM 20726 SG CYS Q 127 94.996 92.349 30.226 1.00 48.38 S ATOM 12262 SG CYS K 127 31.483 32.751 34.149 1.00 47.46 S ATOM 23538 SG CYS S 127 35.389 31.666 31.627 1.00 46.91 S ATOM 12262 SG CYS K 127 31.483 32.751 34.149 1.00 47.46 S ATOM 26357 SG CYS U 127 32.566 35.215 30.125 1.00 47.87 S ATOM 6624 SG CYS G 127 94.590 35.355 94.952 1.00 49.43 S ATOM 5218 SG CYS E 127 92.355 94.898 95.060 1.00 49.62 S ATOM 30589 SG CYS B 127 96.337 92.604 93.409 1.00 50.22 S ATOM 1000 SG CYS Z 127 35.211 32.539 95.408 1.00 48.90 S ATOM 33401 SG CYS F 127 34.999 96.220 93.578 1.00 51.16 S Time building chain proxies: 16.55, per 1000 atoms: 0.49 Number of scatterers: 33823 At special positions: 0 Unit cell: (128.7, 128.7, 126.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 16 26.01 S 96 16.00 O 6474 8.00 N 6081 7.00 C 21156 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=0, symmetry=0 Time building additional restraints: 13.38 Conformation dependent library (CDL) restraints added in 5.4 seconds 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7842 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'Z' and resid 10 through 38 removed outlier: 4.123A pdb=" N ALA Z 16 " --> pdb=" O GLU Z 12 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN Z 18 " --> pdb=" O GLU Z 14 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE Z 38 " --> pdb=" O LEU Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 71 Processing helix chain 'Z' and resid 72 through 74 No H-bonds generated for 'chain 'Z' and resid 72 through 74' Processing helix chain 'Z' and resid 92 through 121 Processing helix chain 'Z' and resid 123 through 156 removed outlier: 3.948A pdb=" N LEU Z 135 " --> pdb=" O GLU Z 131 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP Z 136 " --> pdb=" O SER Z 132 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS Z 137 " --> pdb=" O HIS Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 170 through 179 removed outlier: 3.619A pdb=" N GLU Z 176 " --> pdb=" O GLU Z 172 " (cutoff:3.500A) Processing helix chain 'Z' and resid 179 through 187 Processing helix chain 'A' and resid 10 through 38 removed outlier: 4.241A pdb=" N ALA A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 71 Processing helix chain 'A' and resid 92 through 121 removed outlier: 3.530A pdb=" N ASN A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 134 through 156 Processing helix chain 'A' and resid 170 through 179 Processing helix chain 'A' and resid 179 through 188 Processing helix chain 'C' and resid 13 through 38 removed outlier: 3.579A pdb=" N ASN C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 74 removed outlier: 3.804A pdb=" N ASP C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 122 removed outlier: 3.535A pdb=" N ASN C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 134 through 156 Processing helix chain 'C' and resid 170 through 179 removed outlier: 3.714A pdb=" N GLU C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 188 removed outlier: 3.690A pdb=" N SER C 188 " --> pdb=" O GLY C 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 39 removed outlier: 4.175A pdb=" N ALA E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 71 Processing helix chain 'E' and resid 92 through 121 removed outlier: 3.519A pdb=" N ASN E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 156 removed outlier: 3.952A pdb=" N LEU E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASP E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS E 137 " --> pdb=" O HIS E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 179 removed outlier: 3.721A pdb=" N GLU E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 188 Processing helix chain 'G' and resid 10 through 39 removed outlier: 4.183A pdb=" N ALA G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN G 18 " --> pdb=" O GLU G 14 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP G 39 " --> pdb=" O GLY G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 71 Processing helix chain 'G' and resid 72 through 74 No H-bonds generated for 'chain 'G' and resid 72 through 74' Processing helix chain 'G' and resid 92 through 121 removed outlier: 3.509A pdb=" N ASN G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 156 removed outlier: 3.945A pdb=" N LEU G 135 " --> pdb=" O GLU G 131 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP G 136 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 137 " --> pdb=" O HIS G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.726A pdb=" N GLU G 176 " --> pdb=" O GLU G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 187 Processing helix chain 'H' and resid 10 through 38 removed outlier: 3.912A pdb=" N ALA H 16 " --> pdb=" O GLU H 12 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 71 Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 92 through 122 removed outlier: 3.529A pdb=" N ASN H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 134 Processing helix chain 'H' and resid 134 through 156 Processing helix chain 'H' and resid 170 through 179 removed outlier: 3.798A pdb=" N GLU H 176 " --> pdb=" O GLU H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 187 Processing helix chain 'I' and resid 10 through 38 removed outlier: 4.191A pdb=" N ALA I 16 " --> pdb=" O GLU I 12 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN I 18 " --> pdb=" O GLU I 14 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE I 38 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 71 Processing helix chain 'I' and resid 72 through 74 No H-bonds generated for 'chain 'I' and resid 72 through 74' Processing helix chain 'I' and resid 92 through 122 Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 134 through 156 Processing helix chain 'I' and resid 170 through 179 removed outlier: 3.797A pdb=" N GLU I 176 " --> pdb=" O GLU I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 187 Processing helix chain 'J' and resid 10 through 15 removed outlier: 3.523A pdb=" N ALA J 15 " --> pdb=" O THR J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 39 removed outlier: 3.571A pdb=" N ASN J 22 " --> pdb=" O ASN J 18 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE J 38 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP J 39 " --> pdb=" O GLY J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 71 Processing helix chain 'J' and resid 92 through 121 Processing helix chain 'J' and resid 123 through 156 removed outlier: 3.942A pdb=" N LEU J 135 " --> pdb=" O GLU J 131 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASP J 136 " --> pdb=" O SER J 132 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS J 137 " --> pdb=" O HIS J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 179 removed outlier: 3.694A pdb=" N GLU J 176 " --> pdb=" O GLU J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 188 Processing helix chain 'K' and resid 10 through 38 removed outlier: 3.832A pdb=" N ALA K 16 " --> pdb=" O GLU K 12 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN K 18 " --> pdb=" O GLU K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 71 Processing helix chain 'K' and resid 72 through 74 No H-bonds generated for 'chain 'K' and resid 72 through 74' Processing helix chain 'K' and resid 92 through 121 Processing helix chain 'K' and resid 123 through 156 removed outlier: 3.963A pdb=" N LEU K 135 " --> pdb=" O GLU K 131 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASP K 136 " --> pdb=" O SER K 132 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS K 137 " --> pdb=" O HIS K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 179 removed outlier: 3.766A pdb=" N GLU K 176 " --> pdb=" O GLU K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 187 Processing helix chain 'L' and resid 10 through 38 removed outlier: 4.051A pdb=" N ALA L 16 " --> pdb=" O GLU L 12 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN L 18 " --> pdb=" O GLU L 14 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 73 Processing helix chain 'L' and resid 92 through 122 Processing helix chain 'L' and resid 123 through 134 Processing helix chain 'L' and resid 134 through 155 Processing helix chain 'L' and resid 170 through 179 removed outlier: 3.843A pdb=" N GLU L 176 " --> pdb=" O GLU L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 187 Processing helix chain 'M' and resid 10 through 38 removed outlier: 3.874A pdb=" N ALA M 16 " --> pdb=" O GLU M 12 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN M 18 " --> pdb=" O GLU M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 71 Processing helix chain 'M' and resid 72 through 74 No H-bonds generated for 'chain 'M' and resid 72 through 74' Processing helix chain 'M' and resid 92 through 121 Processing helix chain 'M' and resid 123 through 156 removed outlier: 3.965A pdb=" N LEU M 135 " --> pdb=" O GLU M 131 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASP M 136 " --> pdb=" O SER M 132 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS M 137 " --> pdb=" O HIS M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 179 removed outlier: 3.766A pdb=" N GLU M 176 " --> pdb=" O GLU M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 188 removed outlier: 3.541A pdb=" N SER M 188 " --> pdb=" O GLY M 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 15 Processing helix chain 'N' and resid 15 through 38 Processing helix chain 'N' and resid 45 through 73 removed outlier: 3.828A pdb=" N ASP N 72 " --> pdb=" O GLU N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 121 Processing helix chain 'N' and resid 123 through 134 Processing helix chain 'N' and resid 134 through 155 Processing helix chain 'N' and resid 170 through 179 removed outlier: 3.877A pdb=" N GLU N 176 " --> pdb=" O GLU N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 188 removed outlier: 3.613A pdb=" N SER N 188 " --> pdb=" O GLY N 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 38 removed outlier: 4.188A pdb=" N ALA O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN O 18 " --> pdb=" O GLU O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 73 Processing helix chain 'O' and resid 92 through 122 Processing helix chain 'O' and resid 123 through 134 Processing helix chain 'O' and resid 134 through 156 removed outlier: 3.548A pdb=" N ARG O 154 " --> pdb=" O THR O 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 179 removed outlier: 3.865A pdb=" N GLU O 176 " --> pdb=" O GLU O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 188 Processing helix chain 'P' and resid 10 through 38 removed outlier: 3.835A pdb=" N ALA P 16 " --> pdb=" O GLU P 12 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN P 18 " --> pdb=" O GLU P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 71 Processing helix chain 'P' and resid 72 through 74 No H-bonds generated for 'chain 'P' and resid 72 through 74' Processing helix chain 'P' and resid 92 through 121 Processing helix chain 'P' and resid 123 through 156 removed outlier: 3.964A pdb=" N LEU P 135 " --> pdb=" O GLU P 131 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP P 136 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS P 137 " --> pdb=" O HIS P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 170 through 179 removed outlier: 3.774A pdb=" N GLU P 176 " --> pdb=" O GLU P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 188 Processing helix chain 'Q' and resid 10 through 40 removed outlier: 3.910A pdb=" N ALA Q 16 " --> pdb=" O GLU Q 12 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN Q 18 " --> pdb=" O GLU Q 14 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE Q 38 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 71 Processing helix chain 'Q' and resid 72 through 74 No H-bonds generated for 'chain 'Q' and resid 72 through 74' Processing helix chain 'Q' and resid 92 through 121 removed outlier: 3.506A pdb=" N ASN Q 106 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 134 Processing helix chain 'Q' and resid 134 through 156 removed outlier: 3.574A pdb=" N HIS Q 148 " --> pdb=" O LYS Q 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 170 through 179 removed outlier: 3.825A pdb=" N GLU Q 176 " --> pdb=" O GLU Q 172 " (cutoff:3.500A) Processing helix chain 'Q' and resid 179 through 187 Processing helix chain 'R' and resid 10 through 15 Processing helix chain 'R' and resid 15 through 38 removed outlier: 3.523A pdb=" N PHE R 38 " --> pdb=" O LEU R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 71 Processing helix chain 'R' and resid 72 through 74 No H-bonds generated for 'chain 'R' and resid 72 through 74' Processing helix chain 'R' and resid 92 through 122 Processing helix chain 'R' and resid 123 through 156 removed outlier: 3.952A pdb=" N LEU R 135 " --> pdb=" O GLU R 131 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASP R 136 " --> pdb=" O SER R 132 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS R 137 " --> pdb=" O HIS R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 179 removed outlier: 3.704A pdb=" N GLU R 176 " --> pdb=" O GLU R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 188 Processing helix chain 'S' and resid 10 through 38 removed outlier: 4.081A pdb=" N ALA S 16 " --> pdb=" O GLU S 12 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN S 18 " --> pdb=" O GLU S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 71 Processing helix chain 'S' and resid 72 through 74 No H-bonds generated for 'chain 'S' and resid 72 through 74' Processing helix chain 'S' and resid 92 through 121 removed outlier: 3.523A pdb=" N ASN S 106 " --> pdb=" O ALA S 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 156 removed outlier: 3.928A pdb=" N LEU S 135 " --> pdb=" O GLU S 131 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP S 136 " --> pdb=" O SER S 132 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS S 137 " --> pdb=" O HIS S 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 170 through 179 removed outlier: 3.732A pdb=" N GLU S 176 " --> pdb=" O GLU S 172 " (cutoff:3.500A) Processing helix chain 'S' and resid 179 through 187 Processing helix chain 'T' and resid 10 through 40 removed outlier: 4.131A pdb=" N ALA T 16 " --> pdb=" O GLU T 12 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN T 18 " --> pdb=" O GLU T 14 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP T 39 " --> pdb=" O GLY T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 71 Processing helix chain 'T' and resid 72 through 74 No H-bonds generated for 'chain 'T' and resid 72 through 74' Processing helix chain 'T' and resid 92 through 121 removed outlier: 3.560A pdb=" N ASN T 106 " --> pdb=" O ALA T 102 " (cutoff:3.500A) Processing helix chain 'T' and resid 123 through 156 removed outlier: 3.944A pdb=" N LEU T 135 " --> pdb=" O GLU T 131 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASP T 136 " --> pdb=" O SER T 132 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS T 137 " --> pdb=" O HIS T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 170 through 179 removed outlier: 3.688A pdb=" N GLU T 176 " --> pdb=" O GLU T 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 179 through 187 Processing helix chain 'U' and resid 10 through 38 removed outlier: 4.132A pdb=" N ALA U 16 " --> pdb=" O GLU U 12 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN U 18 " --> pdb=" O GLU U 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE U 38 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 71 Processing helix chain 'U' and resid 72 through 74 No H-bonds generated for 'chain 'U' and resid 72 through 74' Processing helix chain 'U' and resid 92 through 121 removed outlier: 3.550A pdb=" N ASN U 106 " --> pdb=" O ALA U 102 " (cutoff:3.500A) Processing helix chain 'U' and resid 123 through 134 Processing helix chain 'U' and resid 134 through 156 removed outlier: 3.594A pdb=" N LYS U 143 " --> pdb=" O VAL U 139 " (cutoff:3.500A) Processing helix chain 'U' and resid 170 through 179 removed outlier: 3.760A pdb=" N GLU U 176 " --> pdb=" O GLU U 172 " (cutoff:3.500A) Processing helix chain 'U' and resid 179 through 187 Processing helix chain 'V' and resid 10 through 15 removed outlier: 3.522A pdb=" N ALA V 15 " --> pdb=" O THR V 11 " (cutoff:3.500A) Processing helix chain 'V' and resid 15 through 40 Processing helix chain 'V' and resid 45 through 72 removed outlier: 3.899A pdb=" N ASP V 72 " --> pdb=" O GLU V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 92 through 122 Processing helix chain 'V' and resid 123 through 134 Processing helix chain 'V' and resid 134 through 155 Processing helix chain 'V' and resid 170 through 179 removed outlier: 3.836A pdb=" N GLU V 176 " --> pdb=" O GLU V 172 " (cutoff:3.500A) Processing helix chain 'V' and resid 179 through 187 Processing helix chain 'W' and resid 10 through 38 removed outlier: 3.854A pdb=" N ALA W 16 " --> pdb=" O GLU W 12 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN W 18 " --> pdb=" O GLU W 14 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 71 removed outlier: 3.727A pdb=" N GLU W 57 " --> pdb=" O ARG W 53 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU W 58 " --> pdb=" O GLU W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 92 through 121 Processing helix chain 'W' and resid 123 through 156 removed outlier: 3.945A pdb=" N LEU W 135 " --> pdb=" O GLU W 131 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP W 136 " --> pdb=" O SER W 132 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS W 137 " --> pdb=" O HIS W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 170 through 179 removed outlier: 3.784A pdb=" N GLU W 176 " --> pdb=" O GLU W 172 " (cutoff:3.500A) Processing helix chain 'W' and resid 179 through 188 Processing helix chain 'B' and resid 10 through 38 removed outlier: 4.088A pdb=" N ALA B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 73 removed outlier: 3.835A pdb=" N GLU B 57 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 64 " --> pdb=" O ARG B 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 122 removed outlier: 3.504A pdb=" N ASN B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 removed outlier: 3.647A pdb=" N GLU B 131 " --> pdb=" O CYS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.779A pdb=" N GLU B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 187 Processing helix chain 'D' and resid 10 through 38 removed outlier: 4.175A pdb=" N ALA D 16 " --> pdb=" O GLU D 12 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 73 removed outlier: 3.669A pdb=" N GLU D 57 " --> pdb=" O ARG D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 121 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 134 through 156 Processing helix chain 'D' and resid 170 through 179 Processing helix chain 'D' and resid 179 through 186 Processing helix chain 'F' and resid 10 through 38 removed outlier: 4.088A pdb=" N ALA F 16 " --> pdb=" O GLU F 12 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN F 18 " --> pdb=" O GLU F 14 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE F 38 " --> pdb=" O LEU F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 73 Processing helix chain 'F' and resid 92 through 122 removed outlier: 3.692A pdb=" N LEU F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 133 removed outlier: 3.902A pdb=" N GLU F 131 " --> pdb=" O CYS F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 156 removed outlier: 3.727A pdb=" N LYS F 137 " --> pdb=" O HIS F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 179 removed outlier: 3.816A pdb=" N GLU F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 188 removed outlier: 3.606A pdb=" N SER F 188 " --> pdb=" O GLY F 184 " (cutoff:3.500A) 2600 hydrogen bonds defined for protein. 7800 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.24 Time building geometry restraints manager: 14.39 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: 11802 1.34 - 1.46: 7661 1.46 - 1.58: 14728 1.58 - 1.71: 0 1.71 - 1.83: 168 Bond restraints: 34359 Sorted by residual: bond pdb=" CB VAL J 21 " pdb=" CG1 VAL J 21 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.70e+00 bond pdb=" CB VAL V 155 " pdb=" CG2 VAL V 155 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.38e+00 bond pdb=" CB THR F 30 " pdb=" CG2 THR F 30 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.33e+00 bond pdb=" CB VAL N 155 " pdb=" CG2 VAL N 155 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" N VAL N 155 " pdb=" CA VAL N 155 " ideal model delta sigma weight residual 1.474 1.451 0.023 1.57e-02 4.06e+03 2.14e+00 ... (remaining 34354 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.01: 253 106.01 - 113.02: 18805 113.02 - 120.03: 12227 120.03 - 127.03: 14597 127.03 - 134.04: 264 Bond angle restraints: 46146 Sorted by residual: angle pdb=" C LEU T 178 " pdb=" N THR T 179 " pdb=" CA THR T 179 " ideal model delta sigma weight residual 122.17 117.98 4.19 1.54e+00 4.22e-01 7.40e+00 angle pdb=" C LEU R 178 " pdb=" N THR R 179 " pdb=" CA THR R 179 " ideal model delta sigma weight residual 122.17 118.04 4.13 1.54e+00 4.22e-01 7.20e+00 angle pdb=" C LEU K 178 " pdb=" N THR K 179 " pdb=" CA THR K 179 " ideal model delta sigma weight residual 122.17 118.06 4.11 1.54e+00 4.22e-01 7.14e+00 angle pdb=" C ARG C 73 " pdb=" N GLY C 74 " pdb=" CA GLY C 74 " ideal model delta sigma weight residual 123.44 120.47 2.97 1.19e+00 7.06e-01 6.22e+00 angle pdb=" N ARG J 19 " pdb=" CA ARG J 19 " pdb=" C ARG J 19 " ideal model delta sigma weight residual 113.18 110.28 2.90 1.21e+00 6.83e-01 5.76e+00 ... (remaining 46141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 17409 17.99 - 35.98: 2534 35.98 - 53.97: 676 53.97 - 71.96: 90 71.96 - 89.95: 15 Dihedral angle restraints: 20724 sinusoidal: 8625 harmonic: 12099 Sorted by residual: dihedral pdb=" CA ASP D 128 " pdb=" C ASP D 128 " pdb=" N PHE D 129 " pdb=" CA PHE D 129 " ideal model delta harmonic sigma weight residual 180.00 155.52 24.48 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA HIS M 133 " pdb=" C HIS M 133 " pdb=" N TYR M 134 " pdb=" CA TYR M 134 " ideal model delta harmonic sigma weight residual -180.00 -159.93 -20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA HIS J 133 " pdb=" C HIS J 133 " pdb=" N TYR J 134 " pdb=" CA TYR J 134 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 20721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3249 0.037 - 0.073: 1314 0.073 - 0.110: 339 0.110 - 0.147: 32 0.147 - 0.183: 4 Chirality restraints: 4938 Sorted by residual: chirality pdb=" CB VAL N 155 " pdb=" CA VAL N 155 " pdb=" CG1 VAL N 155 " pdb=" CG2 VAL N 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CB VAL V 155 " pdb=" CA VAL V 155 " pdb=" CG1 VAL V 155 " pdb=" CG2 VAL V 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CB VAL L 155 " pdb=" CA VAL L 155 " pdb=" CG1 VAL L 155 " pdb=" CG2 VAL L 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 4935 not shown) Planarity restraints: 6129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 176 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C GLU A 176 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU A 176 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG A 177 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 176 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C GLU D 176 " 0.029 2.00e-02 2.50e+03 pdb=" O GLU D 176 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG D 177 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 70 " -0.006 2.00e-02 2.50e+03 1.12e-02 1.26e+00 pdb=" C GLN G 70 " 0.019 2.00e-02 2.50e+03 pdb=" O GLN G 70 " -0.007 2.00e-02 2.50e+03 pdb=" N ASN G 71 " -0.007 2.00e-02 2.50e+03 ... (remaining 6126 not shown) Histogram of nonbonded interaction distances: 0.98 - 1.77: 6 1.77 - 2.55: 447 2.55 - 3.33: 45791 3.33 - 4.12: 85400 4.12 - 4.90: 167935 Warning: very small nonbonded interaction distances. Nonbonded interactions: 299579 Sorted by model distance: nonbonded pdb="FE FE C 201 " pdb="FE FE F 201 " model vdw 0.983 1.480 nonbonded pdb="FE FE J 201 " pdb="FE FE Q 201 " model vdw 0.990 1.480 nonbonded pdb="FE FE I 201 " pdb="FE FE I 202 " model vdw 0.992 1.480 nonbonded pdb="FE FE S 201 " pdb="FE FE U 201 " model vdw 0.994 1.480 nonbonded pdb="FE FE O 201 " pdb="FE FE B 201 " model vdw 0.998 1.480 ... (remaining 299574 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' and resid 3 through 188) selection = (chain 'B' and resid 3 through 188) selection = (chain 'C' and resid 3 through 188) selection = (chain 'D' and resid 3 through 188) selection = chain 'E' selection = (chain 'F' and resid 3 through 188) selection = chain 'G' selection = (chain 'H' and resid 3 through 188) selection = (chain 'I' and resid 3 through 188) selection = (chain 'J' and resid 3 through 188) selection = chain 'K' selection = (chain 'L' and resid 3 through 188) selection = chain 'M' selection = (chain 'N' and resid 3 through 188) selection = (chain 'O' and resid 3 through 188) selection = chain 'P' selection = (chain 'Q' and resid 3 through 188) selection = (chain 'R' and resid 3 through 188) selection = (chain 'S' and resid 3 through 188) selection = chain 'T' selection = (chain 'U' and resid 3 through 188) selection = (chain 'V' and resid 3 through 188) selection = chain 'W' selection = chain 'Z' } 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=0.50 max=1.00 mean=0.99 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.510 Check model and map are aligned: 0.510 Set scattering table: 0.330 Process input model: 81.880 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 : 0.009 0.054 34359 Z= 0.558 Angle : 0.737 8.292 46146 Z= 0.413 Chirality : 0.040 0.183 4938 Planarity : 0.003 0.017 6129 Dihedral : 17.493 89.945 12882 Min Nonbonded Distance : 0.983 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 8.48 % Allowed : 19.03 % Favored : 72.49 % 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: -3.01 (0.11), residues: 4089 helix: -1.77 (0.07), residues: 3153 sheet: None (None), residues: 0 loop : -2.05 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP R 90 HIS 0.010 0.001 HIS L 115 PHE 0.013 0.002 PHE C 52 TYR 0.014 0.002 TYR D 173 ARG 0.006 0.001 ARG R 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 815 time to evaluate : 3.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8728 (t0) cc_final: 0.8439 (t0) REVERT: E 64 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7342 (tm-30) REVERT: E 81 ASP cc_start: 0.7553 (t0) cc_final: 0.7236 (t70) REVERT: E 108 ASN cc_start: 0.8695 (t0) cc_final: 0.8443 (t0) REVERT: G 22 ASN cc_start: 0.8482 (t0) cc_final: 0.8216 (t0) REVERT: H 108 ASN cc_start: 0.8752 (t0) cc_final: 0.8534 (t0) REVERT: H 145 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7824 (mtp) REVERT: I 145 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7612 (mtp) REVERT: J 108 ASN cc_start: 0.8748 (t0) cc_final: 0.8484 (t0) REVERT: K 108 ASN cc_start: 0.8789 (t0) cc_final: 0.8451 (t0) REVERT: L 108 ASN cc_start: 0.8762 (t0) cc_final: 0.8418 (t0) REVERT: M 108 ASN cc_start: 0.8770 (t0) cc_final: 0.8465 (t0) REVERT: M 144 LYS cc_start: 0.8840 (tptm) cc_final: 0.8546 (mtpp) REVERT: N 107 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8664 (tp) REVERT: N 108 ASN cc_start: 0.8731 (t0) cc_final: 0.8452 (t0) REVERT: N 144 LYS cc_start: 0.8911 (tptm) cc_final: 0.8534 (mtpp) REVERT: O 108 ASN cc_start: 0.8747 (t0) cc_final: 0.8483 (t0) REVERT: Q 108 ASN cc_start: 0.8750 (t0) cc_final: 0.8527 (t0) REVERT: Q 145 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7652 (mtp) REVERT: R 108 ASN cc_start: 0.8733 (t0) cc_final: 0.8418 (t0) REVERT: R 181 LYS cc_start: 0.8425 (tptt) cc_final: 0.8205 (tmtt) REVERT: S 108 ASN cc_start: 0.8701 (t0) cc_final: 0.8379 (t0) REVERT: T 105 LYS cc_start: 0.8402 (mtpt) cc_final: 0.8198 (mtpp) REVERT: V 108 ASN cc_start: 0.8720 (t0) cc_final: 0.8460 (t0) REVERT: B 108 ASN cc_start: 0.8655 (t0) cc_final: 0.8345 (t0) REVERT: D 64 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7220 (tm-30) REVERT: D 68 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6703 (mt-10) REVERT: D 108 ASN cc_start: 0.8762 (t0) cc_final: 0.8451 (t0) REVERT: F 64 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7503 (tm-30) REVERT: F 108 ASN cc_start: 0.8459 (t0) cc_final: 0.8193 (t0) outliers start: 300 outliers final: 246 residues processed: 1076 average time/residue: 0.5252 time to fit residues: 856.1414 Evaluate side-chains 952 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 702 time to evaluate : 3.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 42 ASP Chi-restraints excluded: chain Z residue 71 ASN Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 128 ASP Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain Z residue 139 VAL Chi-restraints excluded: chain Z residue 169 SER Chi-restraints excluded: chain Z residue 176 GLU Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 73 ARG Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 71 ASN Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 127 CYS Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 42 ASP Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 71 ASN Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 83 GLN Chi-restraints excluded: chain O residue 127 CYS Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 71 ASN Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 ASN Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 71 ASN Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 145 MET Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 71 ASN Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 145 MET Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 71 ASN Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 127 CYS Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 43 VAL Chi-restraints excluded: chain W residue 55 LEU Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 89 GLU Chi-restraints excluded: chain W residue 132 SER Chi-restraints excluded: chain W residue 145 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 139 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 2.9990 chunk 309 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 319 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 238 optimal weight: 0.5980 chunk 370 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 8 ASN ** Z 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 83 GLN Z 109 GLN ** Z 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 ASN ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN A 147 ASN A 148 HIS ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 115 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN G 8 ASN G 115 HIS G 147 ASN H 8 ASN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN I 8 ASN ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN I 87 GLN I 108 ASN I 147 ASN J 8 ASN J 22 ASN J 87 GLN ** J 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN J 182 HIS K 8 ASN K 22 ASN K 71 ASN K 83 GLN ** K 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN L 22 ASN ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 GLN L 87 GLN M 8 ASN M 22 ASN M 83 GLN ** M 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 HIS N 8 ASN N 22 ASN ** N 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN N 87 GLN N 109 GLN O 8 ASN O 22 ASN ** O 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN O 87 GLN P 8 ASN P 22 ASN P 83 GLN P 87 GLN ** P 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 GLN Q 8 ASN ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN Q 87 GLN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 ASN R 22 ASN R 87 GLN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN S 87 GLN ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 8 ASN T 87 GLN T 108 ASN T 147 ASN U 8 ASN U 70 GLN U 87 GLN U 108 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 ASN V 22 ASN ** V 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN V 87 GLN ** V 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 8 ASN W 22 ASN W 83 GLN W 182 HIS ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 87 GLN B 115 HIS B 147 ASN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN D 22 ASN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN D 115 HIS D 133 HIS ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 HIS ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN F 22 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS F 147 ASN Total number of N/Q/H flips: 94 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34359 Z= 0.179 Angle : 0.518 8.264 46146 Z= 0.271 Chirality : 0.034 0.145 4938 Planarity : 0.003 0.022 6129 Dihedral : 9.874 66.228 5039 Min Nonbonded Distance : 1.260 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 5.37 % Allowed : 21.85 % Favored : 72.77 % 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: 0.96 (0.13), residues: 4089 helix: 1.24 (0.09), residues: 3243 sheet: None (None), residues: 0 loop : -1.62 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 90 HIS 0.006 0.001 HIS L 115 PHE 0.014 0.001 PHE F 129 TYR 0.010 0.001 TYR C 31 ARG 0.007 0.000 ARG T 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1055 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 64 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6775 (tt0) REVERT: Z 104 GLU cc_start: 0.6607 (mm-30) cc_final: 0.6249 (mm-30) REVERT: Z 105 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7747 (mtpt) REVERT: A 68 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6789 (mt-10) REVERT: A 92 LYS cc_start: 0.7845 (tppt) cc_final: 0.7565 (tppt) REVERT: C 7 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8004 (pp30) REVERT: C 138 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7766 (mm-30) REVERT: E 22 ASN cc_start: 0.8330 (t0) cc_final: 0.8090 (t0) REVERT: E 64 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7542 (tm-30) REVERT: E 104 GLU cc_start: 0.7005 (tp30) cc_final: 0.6663 (tp30) REVERT: E 108 ASN cc_start: 0.8695 (t0) cc_final: 0.8471 (t0) REVERT: G 22 ASN cc_start: 0.8187 (t0) cc_final: 0.7967 (t0) REVERT: G 73 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.8284 (mtp180) REVERT: G 104 GLU cc_start: 0.6996 (tp30) cc_final: 0.6641 (tp30) REVERT: H 53 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.7485 (mtm-85) REVERT: H 105 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7428 (mtpp) REVERT: I 53 ARG cc_start: 0.7783 (mtp-110) cc_final: 0.7413 (mtp180) REVERT: I 105 LYS cc_start: 0.8019 (mtpt) cc_final: 0.7596 (mttp) REVERT: J 6 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.8225 (ttm-80) REVERT: J 64 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6210 (mt-10) REVERT: J 83 GLN cc_start: 0.8082 (tt0) cc_final: 0.7795 (tm-30) REVERT: J 105 LYS cc_start: 0.8119 (mtpt) cc_final: 0.7773 (mttp) REVERT: J 108 ASN cc_start: 0.8660 (t0) cc_final: 0.8441 (t0) REVERT: K 108 ASN cc_start: 0.8594 (t0) cc_final: 0.8330 (t0) REVERT: L 31 TYR cc_start: 0.8780 (m-80) cc_final: 0.8424 (m-80) REVERT: L 108 ASN cc_start: 0.8577 (t0) cc_final: 0.8323 (t0) REVERT: L 181 LYS cc_start: 0.8419 (tptt) cc_final: 0.8205 (tmtt) REVERT: M 108 ASN cc_start: 0.8592 (t0) cc_final: 0.8332 (t0) REVERT: N 31 TYR cc_start: 0.8774 (m-80) cc_final: 0.8459 (m-80) REVERT: N 70 GLN cc_start: 0.8342 (tp-100) cc_final: 0.7454 (tp40) REVERT: O 8 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8756 (t0) REVERT: O 22 ASN cc_start: 0.8324 (t0) cc_final: 0.8093 (t0) REVERT: O 108 ASN cc_start: 0.8650 (t0) cc_final: 0.8405 (t0) REVERT: O 121 ARG cc_start: 0.7388 (ttp80) cc_final: 0.7126 (ttp80) REVERT: P 22 ASN cc_start: 0.8249 (t0) cc_final: 0.8025 (t0) REVERT: P 138 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7705 (mm-30) REVERT: Q 53 ARG cc_start: 0.7740 (mtp-110) cc_final: 0.7285 (mtp180) REVERT: Q 105 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7651 (mttp) REVERT: R 22 ASN cc_start: 0.8243 (t0) cc_final: 0.8029 (t0) REVERT: R 104 GLU cc_start: 0.6567 (tp30) cc_final: 0.6362 (tp30) REVERT: R 108 ASN cc_start: 0.8665 (t0) cc_final: 0.8443 (t0) REVERT: S 59 LYS cc_start: 0.8685 (mmtp) cc_final: 0.8368 (mmtm) REVERT: U 138 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7547 (mm-30) REVERT: V 22 ASN cc_start: 0.8222 (t0) cc_final: 0.7993 (t0) REVERT: V 105 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7664 (mtpp) REVERT: V 145 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7450 (mtp) REVERT: W 105 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7964 (mtpp) REVERT: W 138 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7711 (mm-30) REVERT: B 22 ASN cc_start: 0.8162 (t0) cc_final: 0.7944 (t0) REVERT: D 68 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6581 (mt-10) REVERT: D 73 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.7765 (mtp180) REVERT: D 105 LYS cc_start: 0.7866 (mtpt) cc_final: 0.7657 (mmmt) REVERT: D 108 ASN cc_start: 0.8650 (t0) cc_final: 0.8412 (t0) REVERT: F 22 ASN cc_start: 0.8204 (t0) cc_final: 0.7975 (t0) REVERT: F 64 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7336 (tm-30) outliers start: 190 outliers final: 118 residues processed: 1210 average time/residue: 0.5393 time to fit residues: 1018.5134 Evaluate side-chains 968 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 842 time to evaluate : 3.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 83 GLN Chi-restraints excluded: chain Z residue 128 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 83 GLN Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain P residue 138 GLU Chi-restraints excluded: chain Q residue 7 GLN Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 145 MET Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 138 GLU Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 308 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 371 optimal weight: 6.9990 chunk 400 optimal weight: 3.9990 chunk 330 optimal weight: 7.9990 chunk 368 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 297 optimal weight: 0.3980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 ASN ** Z 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 ASN ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN A 108 ASN C 8 ASN ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 147 ASN E 8 ASN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN G 83 GLN H 8 ASN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN H 148 HIS I 8 ASN ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN I 108 ASN I 148 HIS ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN ** J 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 HIS K 8 ASN K 71 ASN ** K 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 ASN ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN M 71 ASN ** M 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 ASN N 148 HIS ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 ASN ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN P 115 HIS ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN Q 108 ASN Q 147 ASN R 8 ASN ** R 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 71 ASN R 83 GLN R 147 ASN S 8 ASN S 83 GLN S 108 ASN ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 8 ASN ** T 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 108 ASN U 8 ASN U 71 ASN U 108 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 ASN V 71 ASN ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 8 ASN ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 182 HIS B 7 GLN B 8 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN D 8 ASN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 HIS ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34359 Z= 0.201 Angle : 0.522 8.193 46146 Z= 0.267 Chirality : 0.034 0.136 4938 Planarity : 0.003 0.030 6129 Dihedral : 8.314 78.758 4739 Min Nonbonded Distance : 1.249 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 6.25 % Allowed : 23.58 % Favored : 70.17 % 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: 2.26 (0.13), residues: 4089 helix: 2.21 (0.09), residues: 3243 sheet: None (None), residues: 0 loop : -1.42 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 90 HIS 0.007 0.001 HIS L 115 PHE 0.017 0.002 PHE V 69 TYR 0.013 0.001 TYR C 31 ARG 0.007 0.000 ARG T 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 945 time to evaluate : 4.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 64 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6802 (tt0) REVERT: A 68 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6770 (mt-10) REVERT: A 181 LYS cc_start: 0.8309 (tmtt) cc_final: 0.7670 (tppt) REVERT: C 108 ASN cc_start: 0.8757 (t0) cc_final: 0.8537 (t0) REVERT: E 22 ASN cc_start: 0.8335 (t0) cc_final: 0.8067 (t0) REVERT: E 64 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7515 (tm-30) REVERT: E 138 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7815 (mm-30) REVERT: G 22 ASN cc_start: 0.8166 (t0) cc_final: 0.7927 (t0) REVERT: G 73 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.8065 (mtp180) REVERT: G 138 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: I 53 ARG cc_start: 0.7636 (mtp-110) cc_final: 0.6948 (ttm170) REVERT: I 105 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7836 (mtpt) REVERT: J 18 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8371 (m-40) REVERT: K 22 ASN cc_start: 0.8237 (t0) cc_final: 0.7987 (t0) REVERT: K 107 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8488 (mt) REVERT: K 145 MET cc_start: 0.8079 (ttm) cc_final: 0.7716 (mtp) REVERT: L 31 TYR cc_start: 0.8766 (m-80) cc_final: 0.8431 (m-80) REVERT: M 22 ASN cc_start: 0.8261 (t0) cc_final: 0.8028 (t0) REVERT: M 145 MET cc_start: 0.8126 (ttm) cc_final: 0.7889 (mtp) REVERT: N 31 TYR cc_start: 0.8814 (m-80) cc_final: 0.8459 (m-80) REVERT: N 70 GLN cc_start: 0.8182 (tp-100) cc_final: 0.7197 (tp40) REVERT: O 22 ASN cc_start: 0.8219 (t0) cc_final: 0.8004 (t0) REVERT: O 145 MET cc_start: 0.8152 (ttm) cc_final: 0.7868 (mtp) REVERT: P 22 ASN cc_start: 0.8270 (t0) cc_final: 0.8021 (t0) REVERT: P 104 GLU cc_start: 0.7329 (tp30) cc_final: 0.6961 (tp30) REVERT: P 138 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7685 (mm-30) REVERT: Q 53 ARG cc_start: 0.7772 (mtp-110) cc_final: 0.7315 (mtp180) REVERT: Q 105 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7724 (mttp) REVERT: R 22 ASN cc_start: 0.8330 (t0) cc_final: 0.8066 (t0) REVERT: S 108 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8355 (t0) REVERT: T 22 ASN cc_start: 0.8237 (t0) cc_final: 0.7999 (t0) REVERT: U 64 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7388 (tm-30) REVERT: U 105 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7702 (mtpt) REVERT: V 22 ASN cc_start: 0.8205 (t0) cc_final: 0.7985 (t0) REVERT: W 22 ASN cc_start: 0.8161 (t0) cc_final: 0.7892 (t0) REVERT: W 105 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7813 (mtpt) REVERT: B 22 ASN cc_start: 0.8197 (t0) cc_final: 0.7994 (t0) REVERT: D 22 ASN cc_start: 0.8284 (t0) cc_final: 0.8001 (t0) REVERT: D 42 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: D 73 ARG cc_start: 0.8426 (mmm-85) cc_final: 0.8067 (mmt180) outliers start: 221 outliers final: 153 residues processed: 1116 average time/residue: 0.5040 time to fit residues: 865.5154 Evaluate side-chains 1001 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 840 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 61 GLU Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 128 ASP Chi-restraints excluded: chain Z residue 145 MET Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 18 ASN Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 83 GLN Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain P residue 138 GLU Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 108 ASN Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 145 MET Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 249 optimal weight: 0.9980 chunk 372 optimal weight: 3.9990 chunk 394 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 353 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 ASN Z 71 ASN ** Z 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 ASN ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN E 8 ASN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN H 8 ASN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN H 83 GLN I 8 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN ** J 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 HIS ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 71 ASN K 115 HIS ** K 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 HIS M 8 ASN ** M 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 148 HIS ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN P 71 ASN Q 8 ASN ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 ASN ** R 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN S 71 ASN S 108 ASN ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 8 ASN ** T 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 108 ASN ** T 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 8 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 ASN ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 115 HIS ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 182 HIS B 8 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 HIS ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34359 Z= 0.223 Angle : 0.532 8.109 46146 Z= 0.271 Chirality : 0.035 0.128 4938 Planarity : 0.003 0.028 6129 Dihedral : 8.051 85.377 4721 Min Nonbonded Distance : 1.235 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 6.47 % Allowed : 25.45 % Favored : 68.08 % 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: 2.61 (0.13), residues: 4089 helix: 2.46 (0.09), residues: 3273 sheet: None (None), residues: 0 loop : -1.45 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP V 90 HIS 0.008 0.001 HIS L 115 PHE 0.013 0.002 PHE V 36 TYR 0.015 0.001 TYR A 31 ARG 0.006 0.000 ARG H 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 904 time to evaluate : 4.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6684 (mt-10) REVERT: A 108 ASN cc_start: 0.8651 (t0) cc_final: 0.8438 (t0) REVERT: C 105 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7773 (mtpp) REVERT: C 108 ASN cc_start: 0.8744 (t0) cc_final: 0.8523 (t0) REVERT: E 22 ASN cc_start: 0.8315 (t0) cc_final: 0.8061 (t0) REVERT: E 64 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7440 (tm-30) REVERT: E 104 GLU cc_start: 0.7418 (tp30) cc_final: 0.7178 (tp30) REVERT: G 22 ASN cc_start: 0.8189 (t0) cc_final: 0.7934 (t0) REVERT: G 73 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.7961 (mmt180) REVERT: G 104 GLU cc_start: 0.7426 (tp30) cc_final: 0.6838 (tp30) REVERT: G 138 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7762 (mm-30) REVERT: I 105 LYS cc_start: 0.8124 (mtpt) cc_final: 0.7849 (mtpt) REVERT: J 18 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8361 (m-40) REVERT: J 22 ASN cc_start: 0.8535 (t0) cc_final: 0.8287 (t0) REVERT: J 108 ASN cc_start: 0.8640 (t0) cc_final: 0.8398 (t0) REVERT: K 22 ASN cc_start: 0.8228 (t0) cc_final: 0.8007 (t0) REVERT: K 107 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8487 (mt) REVERT: K 145 MET cc_start: 0.7879 (ttm) cc_final: 0.7643 (mtp) REVERT: L 31 TYR cc_start: 0.8797 (m-80) cc_final: 0.8481 (m-80) REVERT: L 105 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7650 (mttp) REVERT: M 22 ASN cc_start: 0.8264 (t0) cc_final: 0.8025 (t0) REVERT: N 70 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7176 (tp40) REVERT: O 22 ASN cc_start: 0.8178 (t0) cc_final: 0.7952 (t0) REVERT: O 83 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7541 (pt0) REVERT: P 22 ASN cc_start: 0.8240 (t0) cc_final: 0.8001 (t0) REVERT: Q 53 ARG cc_start: 0.7787 (mtp-110) cc_final: 0.7316 (mtp180) REVERT: Q 105 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7826 (mtpt) REVERT: R 22 ASN cc_start: 0.8344 (t0) cc_final: 0.8103 (t0) REVERT: S 22 ASN cc_start: 0.8251 (t0) cc_final: 0.8034 (t0) REVERT: S 105 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7931 (mtpt) REVERT: S 108 ASN cc_start: 0.8648 (t160) cc_final: 0.8397 (t0) REVERT: T 22 ASN cc_start: 0.8215 (t0) cc_final: 0.7978 (t0) REVERT: U 105 LYS cc_start: 0.7977 (mtpt) cc_final: 0.7555 (mttp) REVERT: V 22 ASN cc_start: 0.8179 (t0) cc_final: 0.7947 (t0) REVERT: V 83 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7672 (pt0) REVERT: W 22 ASN cc_start: 0.8138 (t0) cc_final: 0.7915 (t0) REVERT: W 31 TYR cc_start: 0.9288 (m-80) cc_final: 0.9060 (m-80) REVERT: W 105 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7826 (mtpp) REVERT: W 108 ASN cc_start: 0.8753 (t0) cc_final: 0.8475 (t0) REVERT: B 105 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7642 (mtpp) REVERT: D 22 ASN cc_start: 0.8321 (t0) cc_final: 0.8031 (t0) REVERT: D 42 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: D 73 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.8095 (mmt180) REVERT: F 105 LYS cc_start: 0.7877 (mtmt) cc_final: 0.7462 (mmmt) outliers start: 229 outliers final: 165 residues processed: 1091 average time/residue: 0.5031 time to fit residues: 846.0568 Evaluate side-chains 998 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 827 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 61 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 128 ASP Chi-restraints excluded: chain Z residue 145 MET Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain J residue 18 ASN Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 83 GLN Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 61 GLU Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 83 GLN Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 83 GLN Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 293 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 336 optimal weight: 1.9990 chunk 272 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 353 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 ASN Z 83 GLN ** Z 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 ASN ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN H 108 ASN I 8 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN ** J 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 HIS K 71 ASN ** K 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 HIS L 8 ASN ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN M 115 HIS ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 ASN ** R 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 8 ASN ** T 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 71 ASN T 108 ASN ** T 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 ASN ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 182 HIS B 8 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34359 Z= 0.235 Angle : 0.541 8.093 46146 Z= 0.275 Chirality : 0.035 0.134 4938 Planarity : 0.003 0.046 6129 Dihedral : 7.920 87.745 4717 Min Nonbonded Distance : 1.227 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 6.96 % Allowed : 25.67 % Favored : 67.37 % 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: 2.85 (0.14), residues: 4089 helix: 2.61 (0.09), residues: 3282 sheet: None (None), residues: 0 loop : -1.34 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 90 HIS 0.008 0.001 HIS L 115 PHE 0.012 0.002 PHE W 36 TYR 0.015 0.001 TYR A 31 ARG 0.007 0.000 ARG H 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1129 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 883 time to evaluate : 4.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 64 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6660 (tt0) REVERT: A 68 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6658 (mt-10) REVERT: A 105 LYS cc_start: 0.8143 (mtpt) cc_final: 0.7706 (mttp) REVERT: C 64 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7279 (tm-30) REVERT: C 108 ASN cc_start: 0.8722 (t0) cc_final: 0.8521 (t0) REVERT: E 22 ASN cc_start: 0.8327 (t0) cc_final: 0.8088 (t0) REVERT: E 64 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7451 (tm-30) REVERT: E 108 ASN cc_start: 0.8725 (t0) cc_final: 0.8522 (t0) REVERT: G 73 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.7976 (mmt180) REVERT: I 53 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7564 (mtm-85) REVERT: J 18 ASN cc_start: 0.8922 (OUTLIER) cc_final: 0.8356 (m-40) REVERT: J 22 ASN cc_start: 0.8550 (t0) cc_final: 0.8286 (t0) REVERT: K 22 ASN cc_start: 0.8282 (t0) cc_final: 0.8040 (t0) REVERT: K 103 MET cc_start: 0.7416 (tpp) cc_final: 0.7165 (tpp) REVERT: L 105 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7676 (mttp) REVERT: M 22 ASN cc_start: 0.8267 (t0) cc_final: 0.8034 (t0) REVERT: N 70 GLN cc_start: 0.8150 (tp-100) cc_final: 0.7042 (tp-100) REVERT: O 22 ASN cc_start: 0.8166 (t0) cc_final: 0.7943 (t0) REVERT: O 83 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: P 22 ASN cc_start: 0.8221 (t0) cc_final: 0.8008 (t0) REVERT: P 105 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7724 (mtpp) REVERT: P 108 ASN cc_start: 0.8718 (t0) cc_final: 0.8509 (t0) REVERT: Q 53 ARG cc_start: 0.7821 (mtp-110) cc_final: 0.7381 (mtp180) REVERT: Q 105 LYS cc_start: 0.8110 (mtpt) cc_final: 0.7780 (mtpt) REVERT: R 8 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8670 (t0) REVERT: R 22 ASN cc_start: 0.8359 (t0) cc_final: 0.8107 (t0) REVERT: S 22 ASN cc_start: 0.8351 (t0) cc_final: 0.8110 (t0) REVERT: S 108 ASN cc_start: 0.8667 (t160) cc_final: 0.8457 (t0) REVERT: T 22 ASN cc_start: 0.8204 (t0) cc_final: 0.7967 (t0) REVERT: U 64 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7426 (tm-30) REVERT: U 105 LYS cc_start: 0.8058 (mtpt) cc_final: 0.7776 (mtpt) REVERT: U 138 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7608 (mm-30) REVERT: V 22 ASN cc_start: 0.8205 (t0) cc_final: 0.7976 (t0) REVERT: V 83 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7766 (pt0) REVERT: W 22 ASN cc_start: 0.8176 (t0) cc_final: 0.7931 (t0) REVERT: W 108 ASN cc_start: 0.8738 (t0) cc_final: 0.8479 (t0) REVERT: B 108 ASN cc_start: 0.8632 (t0) cc_final: 0.8402 (t0) REVERT: D 22 ASN cc_start: 0.8342 (t0) cc_final: 0.8055 (t0) REVERT: D 42 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: D 73 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.8150 (mmt180) REVERT: F 42 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8243 (m-30) REVERT: F 64 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7080 (tm-30) outliers start: 246 outliers final: 184 residues processed: 1079 average time/residue: 0.5051 time to fit residues: 839.2570 Evaluate side-chains 1012 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 820 time to evaluate : 3.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 83 GLN Chi-restraints excluded: chain Z residue 128 ASP Chi-restraints excluded: chain Z residue 145 MET Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain J residue 18 ASN Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 83 GLN Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 83 GLN Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 145 MET Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 61 GLU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 132 SER Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.7980 chunk 355 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 394 optimal weight: 0.9990 chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 ASN Z 22 ASN Z 147 ASN ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 70 GLN C 7 GLN C 8 ASN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 70 GLN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN ** J 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 GLN ** R 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN S 147 ASN ** T 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 8 ASN T 70 GLN T 108 ASN ** T 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 71 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 ASN ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 182 HIS B 8 ASN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN D 147 ASN ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34359 Z= 0.182 Angle : 0.521 8.048 46146 Z= 0.266 Chirality : 0.034 0.137 4938 Planarity : 0.003 0.031 6129 Dihedral : 7.412 84.958 4710 Min Nonbonded Distance : 1.263 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 6.14 % Allowed : 25.93 % Favored : 67.94 % 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: 3.18 (0.14), residues: 4089 helix: 2.87 (0.09), residues: 3291 sheet: None (None), residues: 0 loop : -1.43 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 90 HIS 0.008 0.001 HIS L 115 PHE 0.011 0.001 PHE F 129 TYR 0.015 0.001 TYR A 31 ARG 0.009 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 925 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6798 (mt-10) REVERT: A 105 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7664 (mtpp) REVERT: C 64 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7308 (tm-30) REVERT: C 83 GLN cc_start: 0.8282 (pt0) cc_final: 0.8028 (pt0) REVERT: C 105 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7773 (mtpt) REVERT: E 22 ASN cc_start: 0.8253 (t0) cc_final: 0.8037 (t0) REVERT: E 105 LYS cc_start: 0.7933 (mtpt) cc_final: 0.7632 (mtpt) REVERT: E 108 ASN cc_start: 0.8725 (t0) cc_final: 0.8521 (t0) REVERT: G 73 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7887 (mmt180) REVERT: G 105 LYS cc_start: 0.8049 (mtpt) cc_final: 0.7788 (mtpp) REVERT: H 70 GLN cc_start: 0.8476 (tp-100) cc_final: 0.7733 (tp-100) REVERT: I 53 ARG cc_start: 0.8149 (mmm-85) cc_final: 0.7678 (mtm-85) REVERT: J 18 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8322 (m-40) REVERT: J 22 ASN cc_start: 0.8432 (t0) cc_final: 0.8186 (t0) REVERT: K 68 GLU cc_start: 0.7440 (tp30) cc_final: 0.7185 (tp30) REVERT: M 22 ASN cc_start: 0.8199 (t0) cc_final: 0.7969 (t0) REVERT: N 67 LEU cc_start: 0.8991 (mt) cc_final: 0.8787 (mt) REVERT: N 70 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7110 (tp-100) REVERT: O 83 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: P 105 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7755 (mtpt) REVERT: Q 53 ARG cc_start: 0.7803 (mtp-110) cc_final: 0.7391 (mtp180) REVERT: Q 105 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7812 (mtpt) REVERT: R 31 TYR cc_start: 0.9203 (m-80) cc_final: 0.8997 (m-80) REVERT: R 68 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6838 (mp0) REVERT: R 105 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7885 (mtpp) REVERT: S 22 ASN cc_start: 0.8282 (t0) cc_final: 0.8064 (t0) REVERT: U 105 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7762 (mtpp) REVERT: U 138 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: V 22 ASN cc_start: 0.8226 (t0) cc_final: 0.8025 (t0) REVERT: V 83 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7630 (pt0) REVERT: V 108 ASN cc_start: 0.8654 (t0) cc_final: 0.8415 (t0) REVERT: W 22 ASN cc_start: 0.8057 (t0) cc_final: 0.7852 (t0) REVERT: B 108 ASN cc_start: 0.8607 (t0) cc_final: 0.8388 (t0) REVERT: D 22 ASN cc_start: 0.8251 (t0) cc_final: 0.7998 (t0) REVERT: D 53 ARG cc_start: 0.7818 (ttp-110) cc_final: 0.7531 (ttm110) REVERT: D 64 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7179 (tm-30) REVERT: D 68 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6599 (mt-10) REVERT: D 92 LYS cc_start: 0.7362 (pttm) cc_final: 0.7091 (pttm) REVERT: D 105 LYS cc_start: 0.8058 (mtpt) cc_final: 0.7730 (mtpp) REVERT: F 105 LYS cc_start: 0.7914 (mtpt) cc_final: 0.7573 (mtpp) outliers start: 217 outliers final: 174 residues processed: 1092 average time/residue: 0.5060 time to fit residues: 847.3502 Evaluate side-chains 1008 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 829 time to evaluate : 3.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ASN Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 128 ASP Chi-restraints excluded: chain Z residue 145 MET Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 18 ASN Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 70 GLN Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 83 GLN Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain R residue 7 GLN Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 83 GLN Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain U residue 145 MET Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 61 GLU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 132 SER Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 332 optimal weight: 0.8980 chunk 220 optimal weight: 9.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 0.3980 chunk 239 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 ASN Z 148 HIS ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN C 8 ASN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 HIS H 8 ASN ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 HIS ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN J 71 ASN J 115 HIS ** K 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 182 HIS ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 ASN ** R 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 HIS ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN ** T 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 8 ASN T 108 ASN ** T 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 133 HIS V 8 ASN V 133 HIS ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 108 ASN ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34359 Z= 0.237 Angle : 0.553 8.122 46146 Z= 0.281 Chirality : 0.035 0.147 4938 Planarity : 0.003 0.047 6129 Dihedral : 7.232 84.998 4702 Min Nonbonded Distance : 1.229 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 6.33 % Allowed : 26.41 % Favored : 67.26 % 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: 3.20 (0.14), residues: 4089 helix: 2.85 (0.09), residues: 3282 sheet: None (None), residues: 0 loop : -1.23 (0.24), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 90 HIS 0.008 0.001 HIS L 115 PHE 0.011 0.002 PHE U 36 TYR 0.019 0.001 TYR P 31 ARG 0.007 0.000 ARG E 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 879 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 31 TYR cc_start: 0.9188 (m-80) cc_final: 0.8962 (m-80) REVERT: Z 108 ASN cc_start: 0.8631 (t0) cc_final: 0.8424 (t0) REVERT: A 68 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6783 (mt-10) REVERT: A 105 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7724 (mtpp) REVERT: C 64 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7286 (tm-30) REVERT: C 83 GLN cc_start: 0.8319 (pt0) cc_final: 0.8079 (pt0) REVERT: E 22 ASN cc_start: 0.8304 (t0) cc_final: 0.8071 (t0) REVERT: E 105 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7708 (mtpp) REVERT: E 108 ASN cc_start: 0.8737 (t0) cc_final: 0.8525 (t0) REVERT: G 73 ARG cc_start: 0.8251 (mmm-85) cc_final: 0.7904 (mmt180) REVERT: G 105 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7880 (mtpp) REVERT: I 53 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7589 (mtm-85) REVERT: J 18 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8356 (m-40) REVERT: J 22 ASN cc_start: 0.8473 (t0) cc_final: 0.8209 (t0) REVERT: K 68 GLU cc_start: 0.7424 (tp30) cc_final: 0.7200 (tp30) REVERT: M 22 ASN cc_start: 0.8305 (t0) cc_final: 0.8078 (t0) REVERT: N 70 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7425 (tp40) REVERT: P 105 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7760 (mtpt) REVERT: Q 53 ARG cc_start: 0.7807 (mtp-110) cc_final: 0.7393 (mtp180) REVERT: R 31 TYR cc_start: 0.9221 (m-80) cc_final: 0.9013 (m-80) REVERT: R 68 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6839 (mp0) REVERT: S 22 ASN cc_start: 0.8345 (t0) cc_final: 0.8083 (t0) REVERT: S 105 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7753 (mtpt) REVERT: T 22 ASN cc_start: 0.8456 (t0) cc_final: 0.8237 (t0) REVERT: U 104 GLU cc_start: 0.7327 (tp30) cc_final: 0.6721 (tp30) REVERT: U 105 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7764 (mtpp) REVERT: U 138 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7650 (mm-30) REVERT: V 22 ASN cc_start: 0.8284 (t0) cc_final: 0.8041 (t0) REVERT: V 83 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7733 (pt0) REVERT: V 108 ASN cc_start: 0.8661 (t0) cc_final: 0.8369 (t0) REVERT: W 22 ASN cc_start: 0.8182 (t0) cc_final: 0.7951 (t0) REVERT: B 108 ASN cc_start: 0.8623 (t0) cc_final: 0.8398 (t0) REVERT: D 22 ASN cc_start: 0.8363 (t0) cc_final: 0.8089 (t0) REVERT: D 53 ARG cc_start: 0.7838 (ttp-110) cc_final: 0.7557 (ttm110) REVERT: D 64 GLU cc_start: 0.7403 (tm-30) cc_final: 0.7171 (tm-30) REVERT: D 68 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6601 (mt-10) REVERT: D 92 LYS cc_start: 0.7336 (pttm) cc_final: 0.7058 (pttp) REVERT: F 64 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7127 (tm-30) REVERT: F 105 LYS cc_start: 0.8018 (mtpt) cc_final: 0.7762 (mtpt) outliers start: 224 outliers final: 183 residues processed: 1054 average time/residue: 0.4952 time to fit residues: 805.4964 Evaluate side-chains 1014 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 827 time to evaluate : 3.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 128 ASP Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 18 ASN Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 145 MET Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 70 GLN Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 83 GLN Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 83 GLN Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 137 LYS Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 61 GLU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 132 SER Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 76 optimal weight: 0.3980 chunk 250 optimal weight: 6.9990 chunk 267 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 309 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 71 ASN ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 71 ASN C 7 GLN C 8 ASN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN H 8 ASN H 22 ASN H 71 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN K 22 ASN ** K 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 ASN ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 ASN R 70 GLN R 71 ASN R 108 ASN ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN ** T 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 8 ASN T 108 ASN ** T 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 ASN V 70 GLN ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 108 ASN W 147 ASN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34359 Z= 0.177 Angle : 0.533 8.121 46146 Z= 0.273 Chirality : 0.034 0.152 4938 Planarity : 0.003 0.037 6129 Dihedral : 6.653 89.873 4695 Min Nonbonded Distance : 1.272 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 5.43 % Allowed : 27.14 % Favored : 67.43 % 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: 3.46 (0.14), residues: 4089 helix: 3.02 (0.09), residues: 3303 sheet: None (None), residues: 0 loop : -1.18 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP K 90 HIS 0.008 0.001 HIS L 115 PHE 0.012 0.001 PHE M 36 TYR 0.017 0.001 TYR P 31 ARG 0.007 0.000 ARG H 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 928 time to evaluate : 4.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 64 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6733 (tt0) REVERT: A 68 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6803 (mt-10) REVERT: A 105 LYS cc_start: 0.7792 (mtpt) cc_final: 0.7420 (mttp) REVERT: A 108 ASN cc_start: 0.8644 (t0) cc_final: 0.8410 (t0) REVERT: C 64 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7335 (tm-30) REVERT: C 83 GLN cc_start: 0.8216 (pt0) cc_final: 0.7938 (pt0) REVERT: C 105 LYS cc_start: 0.8119 (mtpt) cc_final: 0.7728 (mtpt) REVERT: E 70 GLN cc_start: 0.8341 (tp40) cc_final: 0.7649 (tp40) REVERT: E 80 GLN cc_start: 0.7063 (pt0) cc_final: 0.6762 (pt0) REVERT: E 105 LYS cc_start: 0.7889 (mtpt) cc_final: 0.7646 (mtpp) REVERT: G 105 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7816 (mtpp) REVERT: J 18 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8436 (m-40) REVERT: J 22 ASN cc_start: 0.8337 (t0) cc_final: 0.8120 (t0) REVERT: K 103 MET cc_start: 0.7542 (tpp) cc_final: 0.7212 (tpp) REVERT: M 22 ASN cc_start: 0.8246 (t0) cc_final: 0.8013 (t0) REVERT: N 70 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7490 (tp-100) REVERT: Q 53 ARG cc_start: 0.7772 (mtp-110) cc_final: 0.7367 (mtp180) REVERT: Q 105 LYS cc_start: 0.8000 (mtpt) cc_final: 0.7619 (mtpt) REVERT: R 68 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6800 (mp0) REVERT: R 108 ASN cc_start: 0.8640 (t0) cc_final: 0.8371 (t0) REVERT: S 105 LYS cc_start: 0.8098 (mtpt) cc_final: 0.7665 (mtpt) REVERT: T 22 ASN cc_start: 0.8378 (t0) cc_final: 0.8139 (t0) REVERT: T 68 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: T 108 ASN cc_start: 0.8534 (t0) cc_final: 0.8215 (t0) REVERT: U 104 GLU cc_start: 0.7346 (tp30) cc_final: 0.6634 (tp30) REVERT: U 105 LYS cc_start: 0.8063 (mtpt) cc_final: 0.7750 (mtpt) REVERT: V 83 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: V 105 LYS cc_start: 0.7873 (mtpt) cc_final: 0.7650 (mtpt) REVERT: W 108 ASN cc_start: 0.8589 (t0) cc_final: 0.8222 (t0) REVERT: D 42 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7912 (m-30) REVERT: D 68 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6666 (mt-10) REVERT: D 92 LYS cc_start: 0.7381 (pttm) cc_final: 0.7127 (pttp) REVERT: D 108 ASN cc_start: 0.8760 (t0) cc_final: 0.8541 (t0) REVERT: F 42 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8025 (m-30) REVERT: F 64 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6793 (tm-30) REVERT: F 105 LYS cc_start: 0.8002 (mtpt) cc_final: 0.7731 (mtpt) outliers start: 192 outliers final: 159 residues processed: 1073 average time/residue: 0.5286 time to fit residues: 882.2586 Evaluate side-chains 1000 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 834 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 128 ASP Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain J residue 18 ASN Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 70 GLN Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain T residue 68 GLU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 61 GLU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 132 SER Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.0670 chunk 376 optimal weight: 4.9990 chunk 343 optimal weight: 3.9990 chunk 366 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 287 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 331 optimal weight: 7.9990 chunk 346 optimal weight: 6.9990 chunk 365 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 22 ASN ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN C 8 ASN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN ** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN K 22 ASN ** K 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 22 ASN ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN S 148 HIS T 7 GLN T 8 ASN ** T 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 148 HIS ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 ASN ** V 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN B 148 HIS ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34359 Z= 0.178 Angle : 0.554 8.157 46146 Z= 0.283 Chirality : 0.035 0.154 4938 Planarity : 0.003 0.062 6129 Dihedral : 6.352 88.094 4675 Min Nonbonded Distance : 1.286 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 5.00 % Allowed : 28.56 % Favored : 66.44 % 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: 3.52 (0.14), residues: 4089 helix: 3.05 (0.09), residues: 3303 sheet: None (None), residues: 0 loop : -1.13 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP P 90 HIS 0.007 0.001 HIS L 115 PHE 0.020 0.001 PHE T 69 TYR 0.021 0.001 TYR P 31 ARG 0.009 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 910 time to evaluate : 3.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 64 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6682 (tt0) REVERT: Z 108 ASN cc_start: 0.8624 (t0) cc_final: 0.8411 (t0) REVERT: A 68 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6809 (mt-10) REVERT: A 105 LYS cc_start: 0.7859 (mtpt) cc_final: 0.7602 (mtpt) REVERT: C 64 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7423 (tm-30) REVERT: C 105 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7674 (mtpt) REVERT: E 64 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7245 (tm-30) REVERT: E 70 GLN cc_start: 0.8340 (tp40) cc_final: 0.7622 (tp40) REVERT: G 105 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7737 (mtpt) REVERT: I 53 ARG cc_start: 0.8074 (mmm-85) cc_final: 0.7549 (mtm-85) REVERT: K 103 MET cc_start: 0.7534 (tpp) cc_final: 0.7180 (tpp) REVERT: M 22 ASN cc_start: 0.8243 (t0) cc_final: 0.8018 (t0) REVERT: N 70 GLN cc_start: 0.8398 (tp-100) cc_final: 0.7320 (tp-100) REVERT: P 105 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7740 (mtpt) REVERT: Q 53 ARG cc_start: 0.7784 (mtp-110) cc_final: 0.7389 (mtp180) REVERT: Q 105 LYS cc_start: 0.7975 (mtpt) cc_final: 0.7612 (mtpt) REVERT: R 68 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6789 (mp0) REVERT: R 108 ASN cc_start: 0.8657 (t0) cc_final: 0.8356 (t0) REVERT: S 105 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7724 (mtpt) REVERT: T 22 ASN cc_start: 0.8415 (t0) cc_final: 0.8173 (t0) REVERT: T 68 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6583 (mp0) REVERT: T 105 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7615 (mtpt) REVERT: T 108 ASN cc_start: 0.8523 (t0) cc_final: 0.8243 (t0) REVERT: U 22 ASN cc_start: 0.8267 (t0) cc_final: 0.8046 (t0) REVERT: U 105 LYS cc_start: 0.8024 (mtpt) cc_final: 0.7731 (mtpt) REVERT: W 108 ASN cc_start: 0.8623 (t0) cc_final: 0.8306 (t0) REVERT: B 31 TYR cc_start: 0.8904 (m-80) cc_final: 0.8662 (m-80) REVERT: D 64 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6702 (tm-30) REVERT: D 68 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6438 (mt-10) REVERT: D 92 LYS cc_start: 0.7443 (pttm) cc_final: 0.7211 (pttp) REVERT: F 64 GLU cc_start: 0.7372 (tm-30) cc_final: 0.6988 (tm-30) REVERT: F 105 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7785 (mtpt) outliers start: 177 outliers final: 148 residues processed: 1035 average time/residue: 0.4998 time to fit residues: 796.5023 Evaluate side-chains 1010 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 860 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain R residue 22 ASN Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 7 GLN Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 68 GLU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 137 LYS Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 61 GLU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 6.9990 chunk 387 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 269 optimal weight: 0.9980 chunk 406 optimal weight: 0.9990 chunk 374 optimal weight: 3.9990 chunk 323 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 250 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 22 ASN ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 22 ASN ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN ** S 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 GLN T 8 ASN ** T 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 ASN V 22 ASN W 148 HIS ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34359 Z= 0.190 Angle : 0.568 8.156 46146 Z= 0.289 Chirality : 0.035 0.163 4938 Planarity : 0.003 0.033 6129 Dihedral : 6.077 86.333 4664 Min Nonbonded Distance : 1.270 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 4.69 % Allowed : 29.29 % Favored : 66.02 % 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: 3.51 (0.14), residues: 4089 helix: 3.04 (0.09), residues: 3303 sheet: None (None), residues: 0 loop : -1.09 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 90 HIS 0.008 0.001 HIS L 115 PHE 0.019 0.001 PHE T 69 TYR 0.024 0.001 TYR P 31 ARG 0.007 0.000 ARG H 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 874 time to evaluate : 3.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 64 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6652 (tt0) REVERT: Z 108 ASN cc_start: 0.8624 (t0) cc_final: 0.8414 (t0) REVERT: A 68 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6788 (mt-10) REVERT: A 105 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7553 (mttp) REVERT: C 64 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7382 (tm-30) REVERT: E 64 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7363 (tm-30) REVERT: G 105 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7732 (mtpt) REVERT: I 53 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7560 (mtm-85) REVERT: K 22 ASN cc_start: 0.8412 (t0) cc_final: 0.8209 (t0) REVERT: K 103 MET cc_start: 0.7463 (tpp) cc_final: 0.7107 (tpp) REVERT: L 104 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6960 (tp30) REVERT: M 22 ASN cc_start: 0.8308 (t0) cc_final: 0.8091 (t0) REVERT: N 70 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7480 (tp-100) REVERT: P 105 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7746 (mtpt) REVERT: Q 53 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.7391 (mtp180) REVERT: Q 105 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7619 (mtpt) REVERT: R 68 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6819 (mp0) REVERT: R 108 ASN cc_start: 0.8664 (t0) cc_final: 0.8400 (t0) REVERT: S 105 LYS cc_start: 0.8063 (mtpt) cc_final: 0.7734 (mtpt) REVERT: T 22 ASN cc_start: 0.8442 (t0) cc_final: 0.8166 (t0) REVERT: T 68 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: T 105 LYS cc_start: 0.7866 (mtpt) cc_final: 0.7577 (mtpt) REVERT: T 108 ASN cc_start: 0.8547 (t0) cc_final: 0.8256 (t0) REVERT: U 22 ASN cc_start: 0.8286 (t0) cc_final: 0.8062 (t0) REVERT: U 64 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7293 (tm-30) REVERT: U 105 LYS cc_start: 0.8000 (mtpt) cc_final: 0.7737 (mtpt) REVERT: V 145 MET cc_start: 0.8021 (ttm) cc_final: 0.7780 (mtp) REVERT: W 108 ASN cc_start: 0.8605 (t0) cc_final: 0.8280 (t0) REVERT: B 105 LYS cc_start: 0.7968 (mtpt) cc_final: 0.7651 (mtpt) REVERT: D 92 LYS cc_start: 0.7463 (pttm) cc_final: 0.7238 (pttp) REVERT: F 42 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: F 64 GLU cc_start: 0.7257 (tm-30) cc_final: 0.7032 (tm-30) outliers start: 166 outliers final: 151 residues processed: 989 average time/residue: 0.5059 time to fit residues: 770.8576 Evaluate side-chains 1012 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 857 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 83 GLN Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 70 GLN Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 83 GLN Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 7 GLN Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 68 GLU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 137 LYS Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 61 GLU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 3.9990 chunk 344 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 298 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 324 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 22 ASN ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS G 22 ASN G 83 GLN H 8 ASN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 HIS ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 22 ASN ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 GLN S 8 ASN ** S 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 8 ASN ** T 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 ASN ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.137485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.126671 restraints weight = 56268.683| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.92 r_work: 0.3530 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34359 Z= 0.191 Angle : 0.571 8.150 46146 Z= 0.292 Chirality : 0.035 0.159 4938 Planarity : 0.003 0.067 6129 Dihedral : 5.896 84.303 4658 Min Nonbonded Distance : 1.271 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 4.66 % Allowed : 29.32 % Favored : 66.02 % 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: 3.52 (0.14), residues: 4089 helix: 3.04 (0.09), residues: 3303 sheet: None (None), residues: 0 loop : -1.08 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 90 HIS 0.008 0.001 HIS L 115 PHE 0.019 0.001 PHE T 69 TYR 0.027 0.001 TYR P 31 ARG 0.008 0.000 ARG T 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12001.67 seconds wall clock time: 213 minutes 42.44 seconds (12822.44 seconds total)