Starting phenix.real_space_refine (version: dev) on Tue Feb 28 06:04:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5s_20654/02_2023/6u5s_20654_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5s_20654/02_2023/6u5s_20654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5s_20654/02_2023/6u5s_20654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5s_20654/02_2023/6u5s_20654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5s_20654/02_2023/6u5s_20654_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5s_20654/02_2023/6u5s_20654_trim.pdb" } resolution = 3.07 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10724 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 104": "OD1" <-> "OD2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "D PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21461 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 5176 Classifications: {'peptide': 376} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 365} Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 10, 'ASN:plan1': 1, 'ARG:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 5357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 5357 Classifications: {'peptide': 376} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 365} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 5292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 5292 Classifications: {'peptide': 376} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 365} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 125 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 9, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "D" Number of atoms: 5368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 5368 Classifications: {'peptide': 376} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 365} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.71, per 1000 atoms: 0.50 Number of scatterers: 21461 At special positions: 0 Unit cell: (148.174, 128.986, 84.214, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 O 2248 8.00 N 1949 7.00 C 7473 6.00 H 9755 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG E 1 " - " ASN A 355 " " NAG F 1 " - " ASN A 241 " " NAG G 1 " - " ASN B 355 " " NAG H 1 " - " ASN B 241 " " NAG I 1 " - " ASN C 355 " " NAG J 1 " - " ASN C 241 " " NAG K 1 " - " ASN D 355 " " NAG L 1 " - " ASN D 241 " Time building additional restraints: 18.12 Conformation dependent library (CDL) restraints added in 2.3 seconds 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 18 sheets defined 40.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 54 through 68 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 172 through 185 removed outlier: 3.639A pdb=" N GLU A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.691A pdb=" N THR A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 301 Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.843A pdb=" N VAL A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 143 through 157 removed outlier: 4.262A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 removed outlier: 4.128A pdb=" N LEU B 186 " --> pdb=" O GLN B 182 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.559A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 Processing helix chain 'B' and resid 324 through 335 removed outlier: 4.213A pdb=" N GLU B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 54 through 68 Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 155 Processing helix chain 'C' and resid 172 through 185 removed outlier: 3.639A pdb=" N GLU C 185 " --> pdb=" O PHE C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.690A pdb=" N THR C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 301 Processing helix chain 'C' and resid 323 through 334 removed outlier: 3.843A pdb=" N VAL C 327 " --> pdb=" O TRP C 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 143 through 157 removed outlier: 4.263A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 187 removed outlier: 4.128A pdb=" N LEU D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.559A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 Processing helix chain 'D' and resid 324 through 335 removed outlier: 4.213A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 47 removed outlier: 5.853A pdb=" N ILE A 12 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N HIS A 46 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 14 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N ALA A 72 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 164 removed outlier: 6.419A pdb=" N LEU A 136 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 222 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 360 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 339 removed outlier: 3.568A pdb=" N VAL A 338 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.233A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 164 removed outlier: 6.617A pdb=" N LEU B 136 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 219 through 221 removed outlier: 6.485A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 337 through 339 removed outlier: 4.134A pdb=" N LYS B 346 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 42 through 47 removed outlier: 5.855A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N HIS C 46 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE C 14 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 164 removed outlier: 6.419A pdb=" N LEU C 136 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 222 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE C 360 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 337 through 339 removed outlier: 3.568A pdb=" N VAL C 338 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS C 346 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 11 through 13 Processing sheet with id=AB5, first strand: chain 'D' and resid 47 through 49 removed outlier: 6.234A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AB7, first strand: chain 'D' and resid 162 through 164 removed outlier: 6.617A pdb=" N LEU D 136 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 219 through 221 removed outlier: 6.485A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 337 through 339 removed outlier: 4.134A pdb=" N LYS D 346 " --> pdb=" O ILE D 354 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1482 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: 7.65 Time building geometry restraints manager: 18.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9747 1.03 - 1.22: 8 1.22 - 1.42: 5089 1.42 - 1.61: 6809 1.61 - 1.81: 56 Bond restraints: 21709 Sorted by residual: bond pdb=" CG PRO C 319 " pdb=" CD PRO C 319 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.24e-01 bond pdb=" CG PRO D 319 " pdb=" CD PRO D 319 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.19e-01 bond pdb=" CG PRO A 319 " pdb=" CD PRO A 319 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.03e-01 bond pdb=" CG PRO B 319 " pdb=" CD PRO B 319 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.64e-01 bond pdb=" CG PRO D 99 " pdb=" CD PRO D 99 " ideal model delta sigma weight residual 1.503 1.473 0.030 3.40e-02 8.65e+02 7.68e-01 ... (remaining 21704 not shown) Histogram of bond angle deviations from ideal: 71.36 - 83.88: 16 83.88 - 96.41: 0 96.41 - 108.93: 9678 108.93 - 121.46: 24025 121.46 - 133.98: 4695 Bond angle restraints: 38414 Sorted by residual: angle pdb=" N ASP C 171 " pdb=" CA ASP C 171 " pdb=" HA ASP C 171 " ideal model delta sigma weight residual 110.00 71.76 38.24 3.00e+00 1.11e-01 1.63e+02 angle pdb=" CB GLU C 305 " pdb=" CA GLU C 305 " pdb=" HA GLU C 305 " ideal model delta sigma weight residual 109.00 71.36 37.64 3.00e+00 1.11e-01 1.57e+02 angle pdb=" C LYS B 172 " pdb=" CA LYS B 172 " pdb=" HA LYS B 172 " ideal model delta sigma weight residual 109.00 72.25 36.75 3.00e+00 1.11e-01 1.50e+02 angle pdb=" CB GLU B 175 " pdb=" CA GLU B 175 " pdb=" HA GLU B 175 " ideal model delta sigma weight residual 109.00 72.66 36.34 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C GLU C 305 " pdb=" CA GLU C 305 " pdb=" HA GLU C 305 " ideal model delta sigma weight residual 109.00 73.00 36.00 3.00e+00 1.11e-01 1.44e+02 ... (remaining 38409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 8699 21.12 - 42.24: 323 42.24 - 63.36: 33 63.36 - 84.47: 12 84.47 - 105.59: 2 Dihedral angle restraints: 9069 sinusoidal: 3873 harmonic: 5196 Sorted by residual: dihedral pdb=" C1 NAG K 1 " pdb=" C2 NAG K 1 " pdb=" C3 NAG K 1 " pdb=" C4 NAG K 1 " ideal model delta sinusoidal sigma weight residual -50.00 55.59 -105.59 1 2.00e+01 2.50e-03 3.05e+01 dihedral pdb=" C1 NAG G 1 " pdb=" C2 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" C4 NAG G 1 " ideal model delta sinusoidal sigma weight residual -50.00 55.57 -105.57 1 2.00e+01 2.50e-03 3.04e+01 dihedral pdb=" CB CYS B 63 " pdb=" SG CYS B 63 " pdb=" SG CYS B 315 " pdb=" CB CYS B 315 " ideal model delta sinusoidal sigma weight residual -86.00 -131.10 45.10 1 1.00e+01 1.00e-02 2.82e+01 ... (remaining 9066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 1907 0.276 - 0.552: 4 0.552 - 0.828: 0 0.828 - 1.104: 4 1.104 - 1.381: 2 Chirality restraints: 1917 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-02 2.50e+03 4.76e+03 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-02 2.50e+03 4.75e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-02 2.50e+03 2.24e+03 ... (remaining 1914 not shown) Planarity restraints: 3529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A 99 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 98 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO C 99 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO D 99 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " -0.018 5.00e-02 4.00e+02 ... (remaining 3526 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 678 2.16 - 2.77: 39546 2.77 - 3.38: 56499 3.38 - 3.99: 73741 3.99 - 4.60: 116923 Nonbonded interactions: 287387 Sorted by model distance: nonbonded pdb=" H GLU C 305 " pdb=" HA GLU C 305 " model vdw 1.549 1.816 nonbonded pdb=" H LYS B 172 " pdb=" HA LYS B 172 " model vdw 1.561 1.816 nonbonded pdb=" HH TYR B 77 " pdb=" O PHE B 101 " model vdw 1.634 1.850 nonbonded pdb=" HH TYR D 77 " pdb=" O PHE D 101 " model vdw 1.635 1.850 nonbonded pdb=" H ASP C 171 " pdb=" HA ASP C 171 " model vdw 1.642 1.816 ... (remaining 287382 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 140 or (resid 141 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA )) or resid 142 through 233 or (resid 234 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 235 through 385)) selection = (chain 'B' and (resid 10 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 39 through 43 or (resid \ 44 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 45 through 46 or (resid 47 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 48 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 96 \ through 103 or (resid 104 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 105 or (resid 106 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 107 through 142 or (r \ esid 143 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD1 or name CD2 or name H or name HA )) or resid 144 or (resid 145 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 146 \ through 150 or (resid 151 through 152 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 153 through 169 or (resid 170 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 171 through 172 or (resid 173 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 174 through 177 or (resid 178 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 179 \ through 188 or (resid 189 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 190 through 194 or (resid 195 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 196 throug \ h 197 or (resid 198 through 200 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 201 through 206 or (resid 207 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 208 \ or (resid 209 through 210 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 211 through 278 or (resid 279 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name CE or name NZ \ or name H or name HA )) or resid 280 through 300 or (resid 301 through 303 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 304 through 345 or (resid 346 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 347 through 368 or (resid 369 through 37 \ 0 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 371 through 385)) selection = (chain 'C' and (resid 10 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 39 through 43 or (resid \ 44 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 45 through 46 or (resid 47 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 48 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 96 \ through 103 or (resid 104 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 105 or (resid 106 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 107 through 115 or (r \ esid 116 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 117 through 140 or (resid 141 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or n \ ame NH2 or name H or name HA )) or resid 142 or (resid 143 and (name N or name C \ A or name C or name O or name CB or name CG or name CD1 or name CD2 or name H or \ name HA )) or resid 144 or (resid 145 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 146 through 150 or (resid 151 thro \ ugh 152 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 153 through 169 or (resid 170 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 171 through 188 or (resid 18 \ 9 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 190 through 194 or (resid 195 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 196 through 198 or (resid 199 thro \ ugh 200 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 201 through 208 or (resid 209 through 210 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 211 through 233 \ or (resid 234 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 235 through 385)) selection = (chain 'D' and (resid 10 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 39 through 43 or (resid \ 44 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 45 through 46 or (resid 47 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 48 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 96 \ through 103 or (resid 104 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 105 or (resid 106 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 107 through 140 or (r \ esid 141 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA )) or re \ sid 142 or (resid 143 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name H or name HA )) or resid 144 or (resid 14 \ 5 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 146 through 150 or (resid 151 through 152 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 153 through 169 or (re \ sid 170 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 171 through 172 or (resid 173 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 174 through 177 or (resid 17 \ 8 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 179 through 188 or (resid 189 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 190 through 194 or (resid 195 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 196 through 197 or (resid 198 through 200 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 201 through 206 or (resid 20 \ 7 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 208 or (resid 209 through 210 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 211 through 233 or (resid 234 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 235 through 300 or (resid 301 through 303 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 304 through 351 or (resid 35 \ 2 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name CE or name NZ or name H or name HA )) or resid 353 through 368 or (resid 3 \ 69 through 370 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 371 through 385)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } 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: 5 Type Number sf(0) Gaussians S 36 5.16 5 C 7473 2.51 5 N 1949 2.21 5 O 2248 1.98 5 H 9755 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.340 Extract box with map and model: 11.790 Check model and map are aligned: 0.300 Process input model: 67.360 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.220 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.003 0.030 11954 Z= 0.213 Angle : 0.405 4.888 16272 Z= 0.251 Chirality : 0.074 1.381 1917 Planarity : 0.002 0.038 2069 Dihedral : 12.044 105.592 4156 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.19), residues: 1496 helix: -0.51 (0.20), residues: 584 sheet: -3.42 (0.29), residues: 228 loop : -3.15 (0.20), residues: 684 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.4702 time to fit residues: 88.5131 Evaluate side-chains 59 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.789 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 147 GLN A 290 GLN B 344 ASN C 60 ASN C 219 HIS C 290 GLN D 344 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 11954 Z= 0.245 Angle : 0.449 4.233 16272 Z= 0.247 Chirality : 0.043 0.369 1917 Planarity : 0.003 0.035 2069 Dihedral : 6.422 109.192 1758 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.92 (0.22), residues: 1496 helix: 0.64 (0.21), residues: 612 sheet: -2.80 (0.29), residues: 248 loop : -2.56 (0.23), residues: 636 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 61 average time/residue: 0.3820 time to fit residues: 38.4098 Evaluate side-chains 55 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 1.859 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2281 time to fit residues: 3.5275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN B 337 GLN B 344 ASN C 10 ASN D 337 GLN D 344 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 11954 Z= 0.243 Angle : 0.425 4.033 16272 Z= 0.235 Chirality : 0.042 0.375 1917 Planarity : 0.003 0.032 2069 Dihedral : 6.225 103.982 1758 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.39 (0.22), residues: 1496 helix: 1.03 (0.22), residues: 612 sheet: -2.38 (0.31), residues: 248 loop : -2.30 (0.23), residues: 636 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 52 average time/residue: 0.4033 time to fit residues: 34.0837 Evaluate side-chains 44 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 1.845 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2200 time to fit residues: 3.1123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS D 10 ASN D 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 11954 Z= 0.342 Angle : 0.481 4.176 16272 Z= 0.265 Chirality : 0.046 0.475 1917 Planarity : 0.003 0.036 2069 Dihedral : 6.396 104.954 1758 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.24 (0.22), residues: 1496 helix: 1.03 (0.22), residues: 620 sheet: -2.37 (0.31), residues: 264 loop : -2.04 (0.23), residues: 612 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 47 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 0.3662 time to fit residues: 29.6088 Evaluate side-chains 40 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 1.809 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2617 time to fit residues: 3.4827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 11954 Z= 0.230 Angle : 0.420 4.047 16272 Z= 0.231 Chirality : 0.044 0.452 1917 Planarity : 0.003 0.037 2069 Dihedral : 6.283 103.419 1758 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.85 (0.22), residues: 1496 helix: 1.32 (0.22), residues: 612 sheet: -1.98 (0.32), residues: 248 loop : -1.87 (0.24), residues: 636 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 40 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.3436 time to fit residues: 23.9299 Evaluate side-chains 38 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.637 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.0040 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 11954 Z= 0.171 Angle : 0.392 4.021 16272 Z= 0.215 Chirality : 0.042 0.373 1917 Planarity : 0.002 0.035 2069 Dihedral : 6.218 103.272 1758 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.22), residues: 1496 helix: 1.51 (0.22), residues: 620 sheet: -1.84 (0.32), residues: 248 loop : -1.72 (0.24), residues: 628 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 46 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 1.816 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.3801 time to fit residues: 29.4374 Evaluate side-chains 41 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.778 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 11954 Z= 0.203 Angle : 0.406 4.833 16272 Z= 0.222 Chirality : 0.043 0.466 1917 Planarity : 0.003 0.036 2069 Dihedral : 6.187 102.685 1758 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.39 (0.23), residues: 1496 helix: 1.61 (0.22), residues: 616 sheet: -1.77 (0.32), residues: 248 loop : -1.52 (0.24), residues: 632 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 42 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 1.610 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.3537 time to fit residues: 25.0126 Evaluate side-chains 41 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 90 optimal weight: 0.0670 chunk 97 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN D 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 11954 Z= 0.149 Angle : 0.384 4.025 16272 Z= 0.210 Chirality : 0.043 0.424 1917 Planarity : 0.002 0.035 2069 Dihedral : 6.171 102.999 1758 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.20 (0.23), residues: 1496 helix: 1.76 (0.22), residues: 616 sheet: -1.66 (0.32), residues: 248 loop : -1.41 (0.25), residues: 632 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 48 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 1.867 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.3732 time to fit residues: 30.2356 Evaluate side-chains 47 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 1.955 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3401 time to fit residues: 2.9480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 104 optimal weight: 7.9990 chunk 40 optimal weight: 0.3980 chunk 120 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 11954 Z= 0.155 Angle : 0.386 4.734 16272 Z= 0.211 Chirality : 0.044 0.572 1917 Planarity : 0.002 0.035 2069 Dihedral : 6.154 102.848 1758 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.10 (0.23), residues: 1496 helix: 1.82 (0.22), residues: 616 sheet: -1.58 (0.32), residues: 248 loop : -1.34 (0.25), residues: 632 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 46 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.909 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.3752 time to fit residues: 29.5127 Evaluate side-chains 45 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.929 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 11954 Z= 0.221 Angle : 0.413 4.583 16272 Z= 0.226 Chirality : 0.045 0.590 1917 Planarity : 0.003 0.037 2069 Dihedral : 6.194 102.850 1758 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.02 (0.23), residues: 1496 helix: 2.11 (0.22), residues: 588 sheet: -1.60 (0.32), residues: 248 loop : -1.36 (0.24), residues: 660 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 48 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.780 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.3630 time to fit residues: 30.0370 Evaluate side-chains 45 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.849 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 120 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.093809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.074099 restraints weight = 67711.431| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.32 r_work: 0.3027 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 11954 Z= 0.201 Angle : 0.401 4.632 16272 Z= 0.220 Chirality : 0.044 0.480 1917 Planarity : 0.003 0.037 2069 Dihedral : 6.202 102.908 1758 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.08 (0.23), residues: 1496 helix: 2.16 (0.22), residues: 588 sheet: -1.52 (0.32), residues: 248 loop : -1.28 (0.24), residues: 660 =============================================================================== Job complete usr+sys time: 3580.93 seconds wall clock time: 65 minutes 41.53 seconds (3941.53 seconds total)