Starting phenix.real_space_refine (version: dev) on Tue Dec 20 13:31:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsx_22462/12_2022/7jsx_22462_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsx_22462/12_2022/7jsx_22462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsx_22462/12_2022/7jsx_22462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsx_22462/12_2022/7jsx_22462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsx_22462/12_2022/7jsx_22462_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsx_22462/12_2022/7jsx_22462_updated.pdb" } resolution = 2.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ASP 28": "OD1" <-> "OD2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "D PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 187": "NH1" <-> "NH2" Residue "E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 305": "NH1" <-> "NH2" Residue "E PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 360": "NH1" <-> "NH2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 13": "OE1" <-> "OE2" Residue "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 125": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 79": "NH1" <-> "NH2" Residue "G TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "G ARG 187": "NH1" <-> "NH2" Residue "G PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 305": "NH1" <-> "NH2" Residue "G PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 360": "NH1" <-> "NH2" Residue "H PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "I ARG 21": "NH1" <-> "NH2" Residue "I ARG 79": "NH1" <-> "NH2" Residue "I TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 131": "NH1" <-> "NH2" Residue "I ARG 187": "NH1" <-> "NH2" Residue "I PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 305": "NH1" <-> "NH2" Residue "I PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 360": "NH1" <-> "NH2" Residue "J PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 125": "NH1" <-> "NH2" Residue "K ARG 21": "NH1" <-> "NH2" Residue "K ARG 79": "NH1" <-> "NH2" Residue "K TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 131": "NH1" <-> "NH2" Residue "K ARG 187": "NH1" <-> "NH2" Residue "K PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 305": "NH1" <-> "NH2" Residue "K PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 360": "NH1" <-> "NH2" Residue "L PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 13": "OE1" <-> "OE2" Residue "L TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "L TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 125": "NH1" <-> "NH2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 79": "NH1" <-> "NH2" Residue "M TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "M ARG 187": "NH1" <-> "NH2" Residue "M PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 305": "NH1" <-> "NH2" Residue "M PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 360": "NH1" <-> "NH2" Residue "N PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 84": "NH1" <-> "NH2" Residue "N ARG 91": "NH1" <-> "NH2" Residue "N TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 125": "NH1" <-> "NH2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O ARG 79": "NH1" <-> "NH2" Residue "O TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 131": "NH1" <-> "NH2" Residue "O ARG 187": "NH1" <-> "NH2" Residue "O PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 360": "NH1" <-> "NH2" Residue "P PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 84": "NH1" <-> "NH2" Residue "P ARG 91": "NH1" <-> "NH2" Residue "P TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 125": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 38813 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "C" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "E" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "G" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "I" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "J" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "K" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "M" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "N" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "O" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "P" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "q" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "r" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "s" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "t" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "u" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "v" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "w" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "x" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "E" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "F" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "G" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "I" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "K" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "L" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "M" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "O" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "P" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Time building chain proxies: 19.87, per 1000 atoms: 0.51 Number of scatterers: 38813 At special positions: 0 Unit cell: (142.636, 142.636, 139.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 280 16.00 O 8045 8.00 N 6632 7.00 C 23856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS C 247 " distance=2.19 Simple disulfide: pdb=" SG CYS E 247 " - pdb=" SG CYS G 247 " distance=2.20 Simple disulfide: pdb=" SG CYS I 247 " - pdb=" SG CYS K 247 " distance=2.20 Simple disulfide: pdb=" SG CYS M 247 " - pdb=" SG CYS O 247 " distance=2.15 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: 16.49 Conformation dependent library (CDL) restraints added in 5.5 seconds 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 32 sheets defined 38.9% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 50 through 59 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 142 through 147 removed outlier: 4.229A pdb=" N THR A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 214 through 232 Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 269 through 272 No H-bonds generated for 'chain 'A' and resid 269 through 272' Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 387 through 394 Processing helix chain 'A' and resid 405 through 408 No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 413 through 432 Processing helix chain 'A' and resid 437 through 451 removed outlier: 6.358A pdb=" N GLY A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TRP A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 47 through 50 No H-bonds generated for 'chain 'B' and resid 47 through 50' Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'C' and resid 50 through 59 Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 113 through 121 Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 142 through 147 removed outlier: 4.225A pdb=" N THR C 147 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 247 through 258 Processing helix chain 'C' and resid 269 through 272 No H-bonds generated for 'chain 'C' and resid 269 through 272' Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'C' and resid 311 through 321 Processing helix chain 'C' and resid 336 through 350 Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 387 through 394 Processing helix chain 'C' and resid 405 through 408 No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 413 through 432 Processing helix chain 'C' and resid 437 through 451 removed outlier: 6.348A pdb=" N GLY C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 460 Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 86 through 99 Processing helix chain 'E' and resid 50 through 59 Processing helix chain 'E' and resid 105 through 107 No H-bonds generated for 'chain 'E' and resid 105 through 107' Processing helix chain 'E' and resid 113 through 121 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 142 through 147 removed outlier: 4.226A pdb=" N THR E 147 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 Processing helix chain 'E' and resid 182 through 194 Processing helix chain 'E' and resid 214 through 232 Processing helix chain 'E' and resid 247 through 258 Processing helix chain 'E' and resid 269 through 272 No H-bonds generated for 'chain 'E' and resid 269 through 272' Processing helix chain 'E' and resid 274 through 287 Processing helix chain 'E' and resid 298 through 302 Processing helix chain 'E' and resid 311 through 321 Processing helix chain 'E' and resid 336 through 350 Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'E' and resid 387 through 394 Processing helix chain 'E' and resid 405 through 408 No H-bonds generated for 'chain 'E' and resid 405 through 408' Processing helix chain 'E' and resid 413 through 432 Processing helix chain 'E' and resid 437 through 451 removed outlier: 6.385A pdb=" N GLY E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP E 443 " --> pdb=" O ARG E 439 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP E 451 " --> pdb=" O SER E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 460 Processing helix chain 'F' and resid 23 through 35 Processing helix chain 'F' and resid 47 through 50 No H-bonds generated for 'chain 'F' and resid 47 through 50' Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 86 through 99 Processing helix chain 'G' and resid 50 through 59 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 142 through 147 removed outlier: 4.217A pdb=" N THR G 147 " --> pdb=" O ALA G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 162 Processing helix chain 'G' and resid 182 through 194 Processing helix chain 'G' and resid 214 through 232 Processing helix chain 'G' and resid 247 through 258 Processing helix chain 'G' and resid 269 through 272 No H-bonds generated for 'chain 'G' and resid 269 through 272' Processing helix chain 'G' and resid 274 through 287 Processing helix chain 'G' and resid 298 through 302 Processing helix chain 'G' and resid 311 through 321 Processing helix chain 'G' and resid 336 through 350 Processing helix chain 'G' and resid 358 through 360 No H-bonds generated for 'chain 'G' and resid 358 through 360' Processing helix chain 'G' and resid 387 through 394 Processing helix chain 'G' and resid 405 through 408 No H-bonds generated for 'chain 'G' and resid 405 through 408' Processing helix chain 'G' and resid 413 through 432 Processing helix chain 'G' and resid 437 through 451 removed outlier: 6.377A pdb=" N GLY G 442 " --> pdb=" O ALA G 438 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASP G 443 " --> pdb=" O ARG G 439 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRP G 451 " --> pdb=" O SER G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 453 through 460 Processing helix chain 'H' and resid 23 through 35 Processing helix chain 'H' and resid 47 through 50 No H-bonds generated for 'chain 'H' and resid 47 through 50' Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 86 through 99 Processing helix chain 'I' and resid 50 through 59 Processing helix chain 'I' and resid 105 through 107 No H-bonds generated for 'chain 'I' and resid 105 through 107' Processing helix chain 'I' and resid 113 through 121 Processing helix chain 'I' and resid 124 through 126 No H-bonds generated for 'chain 'I' and resid 124 through 126' Processing helix chain 'I' and resid 142 through 147 removed outlier: 4.217A pdb=" N THR I 147 " --> pdb=" O ALA I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 162 Processing helix chain 'I' and resid 182 through 194 Processing helix chain 'I' and resid 214 through 232 Processing helix chain 'I' and resid 247 through 258 Processing helix chain 'I' and resid 269 through 272 No H-bonds generated for 'chain 'I' and resid 269 through 272' Processing helix chain 'I' and resid 274 through 287 Processing helix chain 'I' and resid 298 through 302 Processing helix chain 'I' and resid 311 through 321 Processing helix chain 'I' and resid 336 through 350 Processing helix chain 'I' and resid 358 through 360 No H-bonds generated for 'chain 'I' and resid 358 through 360' Processing helix chain 'I' and resid 387 through 394 Processing helix chain 'I' and resid 405 through 408 No H-bonds generated for 'chain 'I' and resid 405 through 408' Processing helix chain 'I' and resid 413 through 432 Processing helix chain 'I' and resid 437 through 451 removed outlier: 6.378A pdb=" N GLY I 442 " --> pdb=" O ALA I 438 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP I 443 " --> pdb=" O ARG I 439 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TRP I 451 " --> pdb=" O SER I 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 453 through 460 Processing helix chain 'J' and resid 23 through 35 Processing helix chain 'J' and resid 47 through 50 No H-bonds generated for 'chain 'J' and resid 47 through 50' Processing helix chain 'J' and resid 55 through 59 Processing helix chain 'J' and resid 86 through 99 Processing helix chain 'K' and resid 50 through 59 Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 121 Processing helix chain 'K' and resid 124 through 126 No H-bonds generated for 'chain 'K' and resid 124 through 126' Processing helix chain 'K' and resid 142 through 147 removed outlier: 4.232A pdb=" N THR K 147 " --> pdb=" O ALA K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 162 Processing helix chain 'K' and resid 182 through 194 Processing helix chain 'K' and resid 214 through 232 Processing helix chain 'K' and resid 247 through 258 Processing helix chain 'K' and resid 269 through 272 No H-bonds generated for 'chain 'K' and resid 269 through 272' Processing helix chain 'K' and resid 274 through 287 Processing helix chain 'K' and resid 298 through 302 Processing helix chain 'K' and resid 311 through 321 Processing helix chain 'K' and resid 336 through 350 Processing helix chain 'K' and resid 358 through 360 No H-bonds generated for 'chain 'K' and resid 358 through 360' Processing helix chain 'K' and resid 387 through 394 Processing helix chain 'K' and resid 405 through 408 No H-bonds generated for 'chain 'K' and resid 405 through 408' Processing helix chain 'K' and resid 413 through 432 Processing helix chain 'K' and resid 437 through 451 removed outlier: 6.409A pdb=" N GLY K 442 " --> pdb=" O ALA K 438 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASP K 443 " --> pdb=" O ARG K 439 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS K 450 " --> pdb=" O ARG K 446 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP K 451 " --> pdb=" O SER K 447 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 460 Processing helix chain 'L' and resid 23 through 35 Processing helix chain 'L' and resid 47 through 50 No H-bonds generated for 'chain 'L' and resid 47 through 50' Processing helix chain 'L' and resid 55 through 59 Processing helix chain 'L' and resid 86 through 99 Processing helix chain 'M' and resid 50 through 59 Processing helix chain 'M' and resid 105 through 107 No H-bonds generated for 'chain 'M' and resid 105 through 107' Processing helix chain 'M' and resid 113 through 121 Processing helix chain 'M' and resid 124 through 126 No H-bonds generated for 'chain 'M' and resid 124 through 126' Processing helix chain 'M' and resid 142 through 147 removed outlier: 4.232A pdb=" N THR M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 162 Processing helix chain 'M' and resid 182 through 194 Processing helix chain 'M' and resid 214 through 232 Processing helix chain 'M' and resid 247 through 258 Processing helix chain 'M' and resid 269 through 272 No H-bonds generated for 'chain 'M' and resid 269 through 272' Processing helix chain 'M' and resid 274 through 287 Processing helix chain 'M' and resid 298 through 302 Processing helix chain 'M' and resid 311 through 321 Processing helix chain 'M' and resid 336 through 350 Processing helix chain 'M' and resid 358 through 360 No H-bonds generated for 'chain 'M' and resid 358 through 360' Processing helix chain 'M' and resid 387 through 394 Processing helix chain 'M' and resid 405 through 408 No H-bonds generated for 'chain 'M' and resid 405 through 408' Processing helix chain 'M' and resid 413 through 432 Processing helix chain 'M' and resid 437 through 451 removed outlier: 6.387A pdb=" N GLY M 442 " --> pdb=" O ALA M 438 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP M 443 " --> pdb=" O ARG M 439 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP M 451 " --> pdb=" O SER M 447 " (cutoff:3.500A) Processing helix chain 'M' and resid 453 through 460 Processing helix chain 'N' and resid 23 through 35 Processing helix chain 'N' and resid 47 through 50 No H-bonds generated for 'chain 'N' and resid 47 through 50' Processing helix chain 'N' and resid 55 through 59 Processing helix chain 'N' and resid 86 through 99 Processing helix chain 'O' and resid 50 through 59 Processing helix chain 'O' and resid 105 through 107 No H-bonds generated for 'chain 'O' and resid 105 through 107' Processing helix chain 'O' and resid 113 through 121 Processing helix chain 'O' and resid 124 through 126 No H-bonds generated for 'chain 'O' and resid 124 through 126' Processing helix chain 'O' and resid 142 through 147 removed outlier: 4.231A pdb=" N THR O 147 " --> pdb=" O ALA O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 162 Processing helix chain 'O' and resid 182 through 194 Processing helix chain 'O' and resid 214 through 232 Processing helix chain 'O' and resid 247 through 258 Processing helix chain 'O' and resid 269 through 272 No H-bonds generated for 'chain 'O' and resid 269 through 272' Processing helix chain 'O' and resid 274 through 287 Processing helix chain 'O' and resid 298 through 302 Processing helix chain 'O' and resid 311 through 321 Processing helix chain 'O' and resid 336 through 350 Processing helix chain 'O' and resid 358 through 360 No H-bonds generated for 'chain 'O' and resid 358 through 360' Processing helix chain 'O' and resid 387 through 394 Processing helix chain 'O' and resid 405 through 408 No H-bonds generated for 'chain 'O' and resid 405 through 408' Processing helix chain 'O' and resid 413 through 432 Processing helix chain 'O' and resid 437 through 451 removed outlier: 6.349A pdb=" N GLY O 442 " --> pdb=" O ALA O 438 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP O 443 " --> pdb=" O ARG O 439 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TRP O 451 " --> pdb=" O SER O 447 " (cutoff:3.500A) Processing helix chain 'O' and resid 453 through 460 Processing helix chain 'P' and resid 23 through 35 Processing helix chain 'P' and resid 47 through 50 No H-bonds generated for 'chain 'P' and resid 47 through 50' Processing helix chain 'P' and resid 55 through 59 Processing helix chain 'P' and resid 86 through 99 Processing helix chain 'q' and resid 126 through 134 Processing helix chain 'r' and resid 126 through 134 Processing helix chain 's' and resid 126 through 134 Processing helix chain 't' and resid 126 through 134 Processing helix chain 'u' and resid 126 through 134 Processing helix chain 'v' and resid 126 through 134 Processing helix chain 'w' and resid 126 through 134 Processing helix chain 'x' and resid 126 through 134 Processing sheet with id= A, first strand: chain 'A' and resid 132 through 139 removed outlier: 6.737A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 37 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 237 through 239 removed outlier: 4.048A pdb=" N THR A 173 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN A 401 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA A 378 " --> pdb=" O GLN A 401 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.235A pdb=" N LEU A 290 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS A 267 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS A 292 " --> pdb=" O HIS A 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 74 through 76 removed outlier: 4.649A pdb=" N LEU B 42 " --> pdb=" O TRP B 76 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU B 107 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU B 122 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA B 109 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLY B 120 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 132 through 139 removed outlier: 6.734A pdb=" N ALA C 39 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU C 138 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU C 37 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP C 86 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 237 through 239 removed outlier: 3.654A pdb=" N THR C 173 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN C 401 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA C 378 " --> pdb=" O GLN C 401 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 264 through 268 removed outlier: 6.234A pdb=" N LEU C 290 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS C 267 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N HIS C 292 " --> pdb=" O HIS C 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 74 through 76 removed outlier: 4.650A pdb=" N LEU D 42 " --> pdb=" O TRP D 76 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU D 107 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU D 122 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ALA D 109 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLY D 120 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 132 through 139 removed outlier: 6.733A pdb=" N ALA E 39 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU E 138 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU E 37 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP E 86 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA E 102 " --> pdb=" O CYS E 84 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N CYS E 84 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 237 through 239 removed outlier: 3.672A pdb=" N THR E 173 " --> pdb=" O PHE E 402 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLN E 401 " --> pdb=" O PRO E 376 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA E 378 " --> pdb=" O GLN E 401 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 264 through 268 removed outlier: 6.233A pdb=" N LEU E 290 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N HIS E 267 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS E 292 " --> pdb=" O HIS E 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 74 through 76 removed outlier: 4.656A pdb=" N LEU F 42 " --> pdb=" O TRP F 76 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU F 107 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU F 122 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA F 109 " --> pdb=" O GLY F 120 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLY F 120 " --> pdb=" O ALA F 109 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 132 through 139 removed outlier: 6.732A pdb=" N ALA G 39 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU G 138 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU G 37 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP G 86 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA G 102 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N CYS G 84 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 237 through 239 removed outlier: 3.694A pdb=" N THR G 173 " --> pdb=" O PHE G 402 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLN G 401 " --> pdb=" O PRO G 376 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA G 378 " --> pdb=" O GLN G 401 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 264 through 268 removed outlier: 6.233A pdb=" N LEU G 290 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N HIS G 267 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS G 292 " --> pdb=" O HIS G 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 74 through 76 removed outlier: 4.652A pdb=" N LEU H 42 " --> pdb=" O TRP H 76 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU H 107 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU H 122 " --> pdb=" O LEU H 107 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA H 109 " --> pdb=" O GLY H 120 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLY H 120 " --> pdb=" O ALA H 109 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 132 through 139 removed outlier: 6.736A pdb=" N ALA I 39 " --> pdb=" O GLU I 136 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU I 138 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU I 37 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP I 86 " --> pdb=" O TYR I 100 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA I 102 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N CYS I 84 " --> pdb=" O ALA I 102 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 237 through 239 removed outlier: 3.662A pdb=" N THR I 173 " --> pdb=" O PHE I 402 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN I 401 " --> pdb=" O PRO I 376 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA I 378 " --> pdb=" O GLN I 401 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 264 through 268 removed outlier: 6.231A pdb=" N LEU I 290 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N HIS I 267 " --> pdb=" O LEU I 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS I 292 " --> pdb=" O HIS I 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'J' and resid 74 through 76 removed outlier: 4.660A pdb=" N LEU J 42 " --> pdb=" O TRP J 76 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU J 107 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU J 122 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA J 109 " --> pdb=" O GLY J 120 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLY J 120 " --> pdb=" O ALA J 109 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 132 through 139 removed outlier: 6.734A pdb=" N ALA K 39 " --> pdb=" O GLU K 136 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU K 138 " --> pdb=" O LEU K 37 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU K 37 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP K 86 " --> pdb=" O TYR K 100 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA K 102 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS K 84 " --> pdb=" O ALA K 102 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 237 through 239 removed outlier: 3.646A pdb=" N THR K 173 " --> pdb=" O PHE K 402 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLN K 401 " --> pdb=" O PRO K 376 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA K 378 " --> pdb=" O GLN K 401 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 264 through 268 removed outlier: 6.236A pdb=" N LEU K 290 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N HIS K 267 " --> pdb=" O LEU K 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS K 292 " --> pdb=" O HIS K 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 74 through 76 removed outlier: 4.648A pdb=" N LEU L 42 " --> pdb=" O TRP L 76 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU L 107 " --> pdb=" O LEU L 122 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU L 122 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA L 109 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLY L 120 " --> pdb=" O ALA L 109 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 132 through 139 removed outlier: 6.737A pdb=" N ALA M 39 " --> pdb=" O GLU M 136 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU M 138 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU M 37 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP M 86 " --> pdb=" O TYR M 100 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA M 102 " --> pdb=" O CYS M 84 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N CYS M 84 " --> pdb=" O ALA M 102 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 237 through 239 removed outlier: 3.658A pdb=" N THR M 173 " --> pdb=" O PHE M 402 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLN M 401 " --> pdb=" O PRO M 376 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA M 378 " --> pdb=" O GLN M 401 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 264 through 268 removed outlier: 6.244A pdb=" N LEU M 290 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS M 267 " --> pdb=" O LEU M 290 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS M 292 " --> pdb=" O HIS M 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'N' and resid 74 through 76 removed outlier: 4.645A pdb=" N LEU N 42 " --> pdb=" O TRP N 76 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU N 107 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU N 122 " --> pdb=" O LEU N 107 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ALA N 109 " --> pdb=" O GLY N 120 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLY N 120 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 132 through 139 removed outlier: 6.740A pdb=" N ALA O 39 " --> pdb=" O GLU O 136 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU O 138 " --> pdb=" O LEU O 37 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU O 37 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP O 86 " --> pdb=" O TYR O 100 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA O 102 " --> pdb=" O CYS O 84 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N CYS O 84 " --> pdb=" O ALA O 102 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 237 through 239 removed outlier: 3.659A pdb=" N THR O 173 " --> pdb=" O PHE O 402 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN O 401 " --> pdb=" O PRO O 376 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA O 378 " --> pdb=" O GLN O 401 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'O' and resid 264 through 268 removed outlier: 6.244A pdb=" N LEU O 290 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N HIS O 267 " --> pdb=" O LEU O 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS O 292 " --> pdb=" O HIS O 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'P' and resid 74 through 76 removed outlier: 4.649A pdb=" N LEU P 42 " --> pdb=" O TRP P 76 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU P 107 " --> pdb=" O LEU P 122 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU P 122 " --> pdb=" O LEU P 107 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA P 109 " --> pdb=" O GLY P 120 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLY P 120 " --> pdb=" O ALA P 109 " (cutoff:3.500A) 1406 hydrogen bonds defined for protein. 4023 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: 13.24 Time building geometry restraints manager: 17.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 6504 1.30 - 1.44: 10625 1.44 - 1.58: 20677 1.58 - 1.72: 351 1.72 - 1.86: 427 Bond restraints: 38584 Sorted by residual: bond pdb=" SD MET E 266 " pdb=" CE MET E 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.91e+01 bond pdb=" SD MET O 266 " pdb=" CE MET O 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.91e+01 bond pdb=" SD MET K 266 " pdb=" CE MET K 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.90e+01 bond pdb=" SD MET M 266 " pdb=" CE MET M 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.90e+01 bond pdb=" SD MET G 266 " pdb=" CE MET G 266 " ideal model delta sigma weight residual 1.791 1.657 0.134 2.50e-02 1.60e+03 2.88e+01 ... (remaining 38579 not shown) Histogram of bond angle deviations from ideal: 92.55 - 100.97: 76 100.97 - 109.40: 5019 109.40 - 117.83: 22860 117.83 - 126.26: 23586 126.26 - 134.69: 771 Bond angle restraints: 52312 Sorted by residual: angle pdb=" N TRP I 66 " pdb=" CA TRP I 66 " pdb=" C TRP I 66 " ideal model delta sigma weight residual 111.36 124.01 -12.65 1.09e+00 8.42e-01 1.35e+02 angle pdb=" N TRP M 66 " pdb=" CA TRP M 66 " pdb=" C TRP M 66 " ideal model delta sigma weight residual 111.36 123.73 -12.37 1.09e+00 8.42e-01 1.29e+02 angle pdb=" N TRP O 66 " pdb=" CA TRP O 66 " pdb=" C TRP O 66 " ideal model delta sigma weight residual 111.36 123.51 -12.15 1.09e+00 8.42e-01 1.24e+02 angle pdb=" N TRP A 66 " pdb=" CA TRP A 66 " pdb=" C TRP A 66 " ideal model delta sigma weight residual 111.36 119.71 -8.35 1.09e+00 8.42e-01 5.87e+01 angle pdb=" N TRP K 66 " pdb=" CA TRP K 66 " pdb=" C TRP K 66 " ideal model delta sigma weight residual 111.36 119.63 -8.27 1.09e+00 8.42e-01 5.76e+01 ... (remaining 52307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.24: 20477 14.24 - 28.49: 2049 28.49 - 42.73: 306 42.73 - 56.97: 88 56.97 - 71.21: 44 Dihedral angle restraints: 22964 sinusoidal: 9084 harmonic: 13880 Sorted by residual: dihedral pdb=" CB CYS M 247 " pdb=" SG CYS M 247 " pdb=" SG CYS O 247 " pdb=" CB CYS O 247 " ideal model delta sinusoidal sigma weight residual -86.00 -36.93 -49.07 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " pdb=" SG CYS C 247 " pdb=" CB CYS C 247 " ideal model delta sinusoidal sigma weight residual -86.00 -37.59 -48.41 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CA PHE H 60 " pdb=" C PHE H 60 " pdb=" N GLY H 61 " pdb=" CA GLY H 61 " ideal model delta harmonic sigma weight residual 180.00 152.45 27.55 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 22961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4358 0.114 - 0.228: 949 0.228 - 0.342: 193 0.342 - 0.456: 68 0.456 - 0.569: 8 Chirality restraints: 5576 Sorted by residual: chirality pdb=" CB ILE G 301 " pdb=" CA ILE G 301 " pdb=" CG1 ILE G 301 " pdb=" CG2 ILE G 301 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 8.11e+00 chirality pdb=" CB ILE K 301 " pdb=" CA ILE K 301 " pdb=" CG1 ILE K 301 " pdb=" CG2 ILE K 301 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" CB ILE E 301 " pdb=" CA ILE E 301 " pdb=" CG1 ILE E 301 " pdb=" CG2 ILE E 301 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.92e+00 ... (remaining 5573 not shown) Planarity restraints: 6856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS I 153 " 0.066 2.00e-02 2.50e+03 5.82e-02 5.08e+01 pdb=" CG HIS I 153 " -0.102 2.00e-02 2.50e+03 pdb=" ND1 HIS I 153 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS I 153 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS I 153 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 HIS I 153 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 153 " -0.066 2.00e-02 2.50e+03 5.81e-02 5.07e+01 pdb=" CG HIS G 153 " 0.101 2.00e-02 2.50e+03 pdb=" ND1 HIS G 153 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS G 153 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 HIS G 153 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS G 153 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 153 " 0.065 2.00e-02 2.50e+03 5.78e-02 5.02e+01 pdb=" CG HIS E 153 " -0.101 2.00e-02 2.50e+03 pdb=" ND1 HIS E 153 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS E 153 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS E 153 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS E 153 " 0.067 2.00e-02 2.50e+03 ... (remaining 6853 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4280 2.74 - 3.28: 40498 3.28 - 3.82: 74775 3.82 - 4.36: 92597 4.36 - 4.90: 145182 Nonbonded interactions: 357332 Sorted by model distance: nonbonded pdb=" NE2 GLN G 156 " pdb=" OD2 ASP G 160 " model vdw 2.201 2.520 nonbonded pdb=" NE2 GLN O 156 " pdb=" OD2 ASP O 160 " model vdw 2.203 2.520 nonbonded pdb=" NE2 GLN I 156 " pdb=" OD2 ASP I 160 " model vdw 2.205 2.520 nonbonded pdb=" NE2 GLN C 156 " pdb=" OD2 ASP C 160 " model vdw 2.206 2.520 nonbonded pdb=" NE2 GLN E 156 " pdb=" OD2 ASP E 160 " model vdw 2.206 2.520 ... (remaining 357327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 280 5.16 5 C 23856 2.51 5 N 6632 2.21 5 O 8045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.850 Construct map_model_manager: 0.000 Extract box with map and model: 10.040 Check model and map are aligned: 0.510 Convert atoms to be neutral: 0.290 Process input model: 93.670 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.022 0.162 38584 Z= 1.423 Angle : 1.671 12.654 52312 Z= 0.981 Chirality : 0.110 0.569 5576 Planarity : 0.014 0.064 6856 Dihedral : 11.972 71.215 14088 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.11), residues: 4760 helix: -0.73 (0.10), residues: 1872 sheet: -0.23 (0.19), residues: 784 loop : -0.64 (0.13), residues: 2104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 805 time to evaluate : 4.415 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 3 residues processed: 848 average time/residue: 1.6462 time to fit residues: 1678.8771 Evaluate side-chains 603 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 600 time to evaluate : 4.399 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 6.0920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 398 optimal weight: 1.9990 chunk 357 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 369 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 275 optimal weight: 0.9990 chunk 428 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 123 ASN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN A 207 ASN ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 267 HIS A 277 ASN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN B 8 ASN B 9 ASN B 29 GLN B 36 ASN C 115 ASN C 123 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 207 ASN C 238 HIS C 241 ASN C 267 HIS C 277 ASN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN C 432 ASN D 8 ASN D 9 ASN D 29 GLN D 36 ASN E 96 GLN E 115 ASN E 123 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN E 207 ASN E 238 HIS E 241 ASN E 267 HIS E 277 ASN E 420 ASN E 432 ASN F 8 ASN F 9 ASN F 29 GLN F 36 ASN G 115 ASN G 123 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN G 207 ASN G 238 HIS G 241 ASN G 267 HIS G 277 ASN G 432 ASN H 8 ASN H 9 ASN H 29 GLN H 36 ASN I 115 ASN I 123 ASN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 ASN I 207 ASN I 238 HIS I 241 ASN I 267 HIS I 277 ASN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 432 ASN J 8 ASN J 9 ASN J 29 GLN J 36 ASN K 96 GLN K 115 ASN K 123 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 163 ASN K 207 ASN ** K 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 241 ASN K 267 HIS K 277 ASN K 420 ASN K 432 ASN L 8 ASN L 9 ASN L 29 GLN M 96 GLN M 115 ASN M 123 ASN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN M 207 ASN M 238 HIS M 241 ASN M 267 HIS M 277 ASN M 420 ASN M 432 ASN N 8 ASN N 9 ASN N 29 GLN N 36 ASN O 115 ASN O 123 ASN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 163 ASN O 207 ASN O 238 HIS O 241 ASN O 267 HIS O 277 ASN O 432 ASN P 8 ASN P 9 ASN P 29 GLN P 36 ASN Total number of N/Q/H flips: 109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 38584 Z= 0.236 Angle : 0.648 5.991 52312 Z= 0.347 Chirality : 0.044 0.196 5576 Planarity : 0.005 0.036 6856 Dihedral : 5.542 23.441 5344 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 0.64 % 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: 0.58 (0.12), residues: 4760 helix: 0.97 (0.11), residues: 1856 sheet: 0.27 (0.18), residues: 696 loop : 0.04 (0.13), residues: 2208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 703 time to evaluate : 4.506 Fit side-chains outliers start: 25 outliers final: 11 residues processed: 705 average time/residue: 1.7377 time to fit residues: 1459.5164 Evaluate side-chains 663 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 652 time to evaluate : 4.916 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 3 residues processed: 9 average time/residue: 0.3787 time to fit residues: 12.9117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 238 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 356 optimal weight: 2.9990 chunk 291 optimal weight: 0.5980 chunk 118 optimal weight: 8.9990 chunk 429 optimal weight: 20.0000 chunk 463 optimal weight: 8.9990 chunk 382 optimal weight: 7.9990 chunk 425 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 344 optimal weight: 10.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 123 ASN A 238 HIS A 420 ASN A 429 GLN B 36 ASN C 45 GLN C 123 ASN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 GLN D 36 ASN D 124 GLN E 45 GLN E 123 ASN E 429 GLN F 36 ASN F 124 GLN G 45 GLN G 123 ASN G 420 ASN G 429 GLN H 36 ASN H 124 GLN I 45 GLN I 123 ASN I 429 GLN J 36 ASN J 124 GLN K 45 GLN K 123 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 HIS K 429 GLN L 36 ASN M 45 GLN M 96 GLN M 123 ASN M 429 GLN N 36 ASN N 124 GLN O 45 GLN O 123 ASN ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 420 ASN O 429 GLN P 8 ASN P 36 ASN P 124 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 38584 Z= 0.395 Angle : 0.769 7.617 52312 Z= 0.413 Chirality : 0.051 0.225 5576 Planarity : 0.006 0.041 6856 Dihedral : 5.858 25.837 5344 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 0.80 % 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: 0.55 (0.12), residues: 4760 helix: 1.02 (0.11), residues: 1904 sheet: -0.21 (0.18), residues: 728 loop : 0.13 (0.13), residues: 2128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 727 time to evaluate : 4.316 Fit side-chains outliers start: 31 outliers final: 16 residues processed: 737 average time/residue: 1.7304 time to fit residues: 1518.3752 Evaluate side-chains 705 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 689 time to evaluate : 4.354 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 10 residues processed: 6 average time/residue: 1.3784 time to fit residues: 16.0891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 424 optimal weight: 0.9990 chunk 322 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 204 optimal weight: 9.9990 chunk 288 optimal weight: 0.9980 chunk 430 optimal weight: 8.9990 chunk 456 optimal weight: 40.0000 chunk 225 optimal weight: 0.9990 chunk 408 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 123 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 123 ASN E 153 HIS F 36 ASN G 96 GLN G 123 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 123 ASN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN K 123 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN L 36 ASN M 95 ASN M 96 GLN M 123 ASN M 153 HIS N 36 ASN O 123 ASN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 38584 Z= 0.210 Angle : 0.583 5.717 52312 Z= 0.311 Chirality : 0.043 0.187 5576 Planarity : 0.004 0.045 6856 Dihedral : 5.316 23.997 5344 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.12), residues: 4760 helix: 1.45 (0.12), residues: 1856 sheet: 0.24 (0.19), residues: 688 loop : 0.25 (0.14), residues: 2216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 706 time to evaluate : 4.505 Fit side-chains outliers start: 26 outliers final: 13 residues processed: 721 average time/residue: 1.6859 time to fit residues: 1454.9785 Evaluate side-chains 690 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 677 time to evaluate : 4.440 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 5.9890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 379 optimal weight: 4.9990 chunk 258 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 339 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 389 optimal weight: 10.0000 chunk 315 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 232 optimal weight: 0.0470 chunk 409 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 123 ASN A 401 GLN B 36 ASN B 115 GLN C 95 ASN C 123 ASN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN E 123 ASN E 156 GLN F 36 ASN G 96 GLN G 123 ASN G 153 HIS G 401 GLN H 36 ASN I 95 ASN I 123 ASN J 36 ASN K 96 GLN K 123 ASN L 36 ASN M 96 GLN M 123 ASN M 401 GLN N 36 ASN O 123 ASN ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 38584 Z= 0.340 Angle : 0.696 6.356 52312 Z= 0.372 Chirality : 0.047 0.219 5576 Planarity : 0.005 0.045 6856 Dihedral : 5.647 26.222 5344 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 1.08 % 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: 0.80 (0.12), residues: 4760 helix: 1.13 (0.12), residues: 1904 sheet: -0.17 (0.18), residues: 736 loop : 0.42 (0.14), residues: 2120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 723 time to evaluate : 4.417 Fit side-chains outliers start: 42 outliers final: 28 residues processed: 753 average time/residue: 1.7040 time to fit residues: 1533.6006 Evaluate side-chains 721 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 693 time to evaluate : 4.854 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 22 residues processed: 6 average time/residue: 0.3592 time to fit residues: 10.6027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 153 optimal weight: 6.9990 chunk 410 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 267 optimal weight: 0.0040 chunk 112 optimal weight: 0.6980 chunk 456 optimal weight: 20.0000 chunk 379 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 239 optimal weight: 6.9990 overall best weight: 3.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 GLN B 36 ASN C 123 ASN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 GLN D 36 ASN D 115 GLN E 96 GLN E 123 ASN E 401 GLN F 36 ASN F 115 GLN G 96 GLN G 401 GLN H 36 ASN H 115 GLN I 96 GLN J 36 ASN J 115 GLN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 GLN L 36 ASN L 115 GLN M 96 GLN M 123 ASN M 401 GLN N 36 ASN O 123 ASN ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 401 GLN P 36 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 38584 Z= 0.321 Angle : 0.669 6.135 52312 Z= 0.358 Chirality : 0.046 0.209 5576 Planarity : 0.005 0.067 6856 Dihedral : 5.565 25.053 5344 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 0.95 % 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: 0.79 (0.12), residues: 4760 helix: 1.13 (0.12), residues: 1904 sheet: -0.34 (0.18), residues: 744 loop : 0.49 (0.14), residues: 2112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 709 time to evaluate : 4.471 Fit side-chains outliers start: 37 outliers final: 30 residues processed: 744 average time/residue: 1.7535 time to fit residues: 1566.0591 Evaluate side-chains 719 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 689 time to evaluate : 4.455 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 30 residues processed: 0 time to fit residues: 5.9621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 440 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 333 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 384 optimal weight: 8.9990 chunk 255 optimal weight: 0.9990 chunk 454 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 chunk 277 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 36 ASN B 115 GLN C 123 ASN C 156 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 GLN D 36 ASN E 96 GLN E 156 GLN E 401 GLN F 36 ASN G 96 GLN G 123 ASN G 156 GLN G 401 GLN H 36 ASN I 96 GLN I 156 GLN J 36 ASN K 96 GLN K 156 GLN L 36 ASN M 95 ASN M 96 GLN M 123 ASN M 156 GLN N 36 ASN O 123 ASN O 156 GLN ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 38584 Z= 0.222 Angle : 0.592 5.824 52312 Z= 0.315 Chirality : 0.043 0.192 5576 Planarity : 0.004 0.030 6856 Dihedral : 5.270 24.132 5344 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.12), residues: 4760 helix: 1.47 (0.12), residues: 1856 sheet: -0.27 (0.18), residues: 736 loop : 0.46 (0.14), residues: 2168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 700 time to evaluate : 4.657 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 35 residues processed: 741 average time/residue: 1.6990 time to fit residues: 1503.4333 Evaluate side-chains 716 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 681 time to evaluate : 3.695 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 31 residues processed: 4 average time/residue: 1.8519 time to fit residues: 13.7942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 281 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 271 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 289 optimal weight: 0.0770 chunk 309 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 357 optimal weight: 9.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 304 GLN B 36 ASN C 123 ASN C 156 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 GLN D 36 ASN E 96 GLN E 123 ASN E 156 GLN E 401 GLN F 36 ASN G 96 GLN G 123 ASN G 156 GLN G 401 GLN H 36 ASN I 123 ASN I 153 HIS I 156 GLN J 36 ASN J 115 GLN K 123 ASN K 153 HIS K 156 GLN L 36 ASN M 96 GLN M 123 ASN M 156 GLN N 36 ASN O 123 ASN O 153 HIS O 156 GLN ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 38584 Z= 0.248 Angle : 0.619 6.165 52312 Z= 0.329 Chirality : 0.044 0.201 5576 Planarity : 0.004 0.031 6856 Dihedral : 5.321 24.462 5344 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.12), residues: 4760 helix: 1.44 (0.12), residues: 1856 sheet: -0.32 (0.18), residues: 736 loop : 0.45 (0.14), residues: 2168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 688 time to evaluate : 4.475 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 31 residues processed: 719 average time/residue: 1.6950 time to fit residues: 1460.9658 Evaluate side-chains 712 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 681 time to evaluate : 4.424 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 31 residues processed: 0 time to fit residues: 6.0042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 413 optimal weight: 4.9990 chunk 435 optimal weight: 1.9990 chunk 397 optimal weight: 7.9990 chunk 423 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 332 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 383 optimal weight: 1.9990 chunk 400 optimal weight: 4.9990 chunk 422 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 36 ASN C 123 ASN C 156 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 GLN D 36 ASN E 96 GLN E 123 ASN E 156 GLN E 401 GLN F 36 ASN G 96 GLN G 156 GLN H 36 ASN I 123 ASN I 156 GLN J 36 ASN K 123 ASN K 156 GLN L 36 ASN M 96 GLN M 156 GLN N 36 ASN O 123 ASN O 156 GLN ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 38584 Z= 0.257 Angle : 0.626 6.163 52312 Z= 0.333 Chirality : 0.045 0.201 5576 Planarity : 0.004 0.030 6856 Dihedral : 5.327 24.501 5344 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 0.80 % 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 (0.12), residues: 4760 helix: 1.42 (0.12), residues: 1856 sheet: -0.32 (0.18), residues: 736 loop : 0.46 (0.14), residues: 2168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 686 time to evaluate : 4.627 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 31 residues processed: 717 average time/residue: 1.7462 time to fit residues: 1496.0686 Evaluate side-chains 712 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 681 time to evaluate : 4.527 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 31 residues processed: 0 time to fit residues: 6.2078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 278 optimal weight: 6.9990 chunk 448 optimal weight: 20.0000 chunk 273 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 311 optimal weight: 7.9990 chunk 470 optimal weight: 10.0000 chunk 432 optimal weight: 9.9990 chunk 374 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 289 optimal weight: 7.9990 chunk 229 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 123 ASN C 156 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 GLN D 36 ASN E 156 GLN E 401 GLN F 36 ASN G 123 ASN G 156 GLN H 36 ASN I 156 GLN J 36 ASN K 123 ASN K 156 GLN L 36 ASN M 123 ASN M 156 GLN N 36 ASN O 123 ASN O 156 GLN ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 38584 Z= 0.337 Angle : 0.698 6.419 52312 Z= 0.372 Chirality : 0.047 0.219 5576 Planarity : 0.005 0.037 6856 Dihedral : 5.541 25.448 5344 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.82 % 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: 0.79 (0.12), residues: 4760 helix: 1.14 (0.12), residues: 1904 sheet: -0.46 (0.18), residues: 744 loop : 0.53 (0.14), residues: 2112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 690 time to evaluate : 4.815 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 31 residues processed: 721 average time/residue: 1.7434 time to fit residues: 1499.3084 Evaluate side-chains 715 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 684 time to evaluate : 4.353 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 31 residues processed: 0 time to fit residues: 6.0861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 297 optimal weight: 3.9990 chunk 398 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 345 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 375 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 385 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 36 ASN B 115 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 156 GLN F 36 ASN G 123 ASN G 156 GLN H 36 ASN I 156 GLN J 36 ASN K 156 GLN L 36 ASN M 123 ASN M 156 GLN N 36 ASN O 123 ASN O 156 GLN ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.156106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.113750 restraints weight = 25641.296| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.01 r_work: 0.2929 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work: 0.2639 rms_B_bonded: 4.66 restraints_weight: 0.1250 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 38584 Z= 0.237 Angle : 0.613 6.059 52312 Z= 0.326 Chirality : 0.044 0.199 5576 Planarity : 0.004 0.030 6856 Dihedral : 5.275 24.089 5344 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 0.82 % 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: 0.95 (0.12), residues: 4760 helix: 1.28 (0.12), residues: 1904 sheet: -0.35 (0.18), residues: 736 loop : 0.59 (0.14), residues: 2120 =============================================================================== Job complete usr+sys time: 20456.00 seconds wall clock time: 359 minutes 44.99 seconds (21584.99 seconds total)