Starting phenix.real_space_refine on Sat Aug 23 23:08:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cxc_7774/08_2025/6cxc_7774_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cxc_7774/08_2025/6cxc_7774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6cxc_7774/08_2025/6cxc_7774_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cxc_7774/08_2025/6cxc_7774_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cxc_7774/08_2025/6cxc_7774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cxc_7774/08_2025/6cxc_7774.map" } resolution = 3.9 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9582 2.51 5 N 2541 2.21 5 O 2989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15196 Number of models: 1 Model: "" Number of chains: 18 Chain: "X" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Y" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 847 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 103} Chain: "G" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "J" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 847 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 103} Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "K" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 847 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 103} Chain: "A" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 580 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "B" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2765 Classifications: {'peptide': 358} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 345} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2733 Classifications: {'peptide': 352} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 580 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "F" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2726 Classifications: {'peptide': 351} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.84, per 1000 atoms: 0.19 Number of scatterers: 15196 At special positions: 0 Unit cell: (153.061, 139.261, 190.699, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2989 8.00 N 2541 7.00 C 9582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS X 20 " - pdb=" SG CYS X 94 " distance=2.04 Simple disulfide: pdb=" SG CYS G 20 " - pdb=" SG CYS G 94 " distance=2.04 Simple disulfide: pdb=" SG CYS I 20 " - pdb=" SG CYS I 94 " distance=2.04 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.04 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS D 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS D 212 " distance=2.03 Simple disulfide: pdb=" SG CYS D 322 " - pdb=" SG CYS D 333 " distance=2.03 Simple disulfide: pdb=" SG CYS D 358 " - pdb=" SG CYS D 367 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 393 " distance=2.03 Simple disulfide: pdb=" SG CYS D 416 " - pdb=" SG CYS D 422 " distance=2.03 Simple disulfide: pdb=" SG CYS E 37 " - pdb=" SG CYS F 439 " distance=2.03 Simple disulfide: pdb=" SG CYS E 69 " - pdb=" SG CYS F 212 " distance=2.03 Simple disulfide: pdb=" SG CYS F 322 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 358 " - pdb=" SG CYS F 367 " distance=2.03 Simple disulfide: pdb=" SG CYS F 382 " - pdb=" SG CYS F 393 " distance=2.03 Simple disulfide: pdb=" SG CYS F 416 " - pdb=" SG CYS F 422 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 NAG-ASN " NAG A 601 " - " ASN A 70 " " NAG C 601 " - " ASN C 70 " " NAG E 601 " - " ASN E 70 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 609.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 34 sheets defined 27.6% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'X' and resid 85 through 89 Processing helix chain 'Y' and resid 164 through 166 No H-bonds generated for 'chain 'Y' and resid 164 through 166' Processing helix chain 'Y' and resid 193 through 197 removed outlier: 3.682A pdb=" N LEU Y 197 " --> pdb=" O SER Y 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 89 Processing helix chain 'J' and resid 164 through 166 No H-bonds generated for 'chain 'J' and resid 164 through 166' Processing helix chain 'J' and resid 193 through 197 removed outlier: 3.681A pdb=" N LEU J 197 " --> pdb=" O SER J 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 89 Processing helix chain 'K' and resid 164 through 166 No H-bonds generated for 'chain 'K' and resid 164 through 166' Processing helix chain 'K' and resid 193 through 197 removed outlier: 3.682A pdb=" N LEU K 197 " --> pdb=" O SER K 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.694A pdb=" N TYR A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 156 through 202 removed outlier: 3.752A pdb=" N GLY B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU B 163 " --> pdb=" O HIS B 159 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 169 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 201 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 removed outlier: 4.416A pdb=" N ASN B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS B 209 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 5.002A pdb=" N GLU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 240 removed outlier: 3.815A pdb=" N ILE B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.534A pdb=" N LEU B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 removed outlier: 4.090A pdb=" N LEU B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.695A pdb=" N VAL B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 removed outlier: 3.533A pdb=" N VAL B 379 " --> pdb=" O PRO B 376 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN B 380 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 383 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 501 removed outlier: 3.627A pdb=" N ASN B 500 " --> pdb=" O ASN B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 4.446A pdb=" N PHE B 505 " --> pdb=" O GLN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 514 Processing helix chain 'C' and resid 82 through 94 removed outlier: 3.732A pdb=" N TYR C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU C 92 " --> pdb=" O ASN C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 176 removed outlier: 3.720A pdb=" N SER D 169 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 202 removed outlier: 3.942A pdb=" N SER D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY D 184 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS D 201 " --> pdb=" O ASN D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 214 removed outlier: 4.054A pdb=" N ASN D 208 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS D 209 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN D 210 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS D 212 " --> pdb=" O ASN D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 227 removed outlier: 4.243A pdb=" N GLU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 240 removed outlier: 3.692A pdb=" N ILE D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 264 removed outlier: 3.571A pdb=" N LEU D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET D 264 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 277 removed outlier: 4.080A pdb=" N LEU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 removed outlier: 3.633A pdb=" N VAL D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 384 removed outlier: 3.571A pdb=" N VAL D 379 " --> pdb=" O PRO D 376 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN D 380 " --> pdb=" O SER D 377 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN D 383 " --> pdb=" O ASN D 380 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 384 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 510 removed outlier: 3.902A pdb=" N ASN D 500 " --> pdb=" O ASN D 496 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 503 " --> pdb=" O ILE D 499 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA D 504 " --> pdb=" O ASN D 500 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE D 505 " --> pdb=" O GLN D 501 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER D 509 " --> pdb=" O PHE D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 514 Processing helix chain 'E' and resid 82 through 94 removed outlier: 3.731A pdb=" N TYR E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS E 87 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU E 92 " --> pdb=" O ASN E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'F' and resid 158 through 202 removed outlier: 3.723A pdb=" N GLY F 162 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU F 163 " --> pdb=" O HIS F 159 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER F 169 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER F 180 " --> pdb=" O LYS F 176 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN F 183 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY F 184 " --> pdb=" O SER F 180 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL F 185 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER F 190 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS F 201 " --> pdb=" O ASN F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 214 removed outlier: 4.037A pdb=" N ASN F 208 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS F 209 " --> pdb=" O PRO F 205 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN F 210 " --> pdb=" O ILE F 206 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS F 212 " --> pdb=" O ASN F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 227 removed outlier: 4.238A pdb=" N GLU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS F 226 " --> pdb=" O GLU F 222 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN F 227 " --> pdb=" O PHE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 240 removed outlier: 3.518A pdb=" N LEU F 231 " --> pdb=" O ASN F 227 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE F 237 " --> pdb=" O ILE F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 264 removed outlier: 3.661A pdb=" N LEU F 260 " --> pdb=" O GLU F 256 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET F 264 " --> pdb=" O LEU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 277 removed outlier: 4.109A pdb=" N LEU F 273 " --> pdb=" O ASP F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.631A pdb=" N VAL F 281 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG F 282 " --> pdb=" O VAL F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 384 removed outlier: 3.572A pdb=" N VAL F 379 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN F 380 " --> pdb=" O SER F 377 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN F 383 " --> pdb=" O ASN F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 510 removed outlier: 3.889A pdb=" N ASN F 500 " --> pdb=" O ASN F 496 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU F 503 " --> pdb=" O ILE F 499 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA F 504 " --> pdb=" O ASN F 500 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE F 505 " --> pdb=" O GLN F 501 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER F 509 " --> pdb=" O PHE F 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 2 through 4 removed outlier: 3.687A pdb=" N CYS X 20 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA X 67 " --> pdb=" O GLN X 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 8 through 10 Processing sheet with id=AA3, first strand: chain 'X' and resid 42 through 49 removed outlier: 6.643A pdb=" N TRP X 34 " --> pdb=" O ILE X 46 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG X 48 " --> pdb=" O MET X 32 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N MET X 32 " --> pdb=" O ARG X 48 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL X 35 " --> pdb=" O PHE X 93 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN X 37 " --> pdb=" O VAL X 91 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL X 91 " --> pdb=" O GLN X 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Y' and resid 119 through 120 removed outlier: 3.611A pdb=" N CYS Y 137 " --> pdb=" O PHE Y 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 167 through 168 removed outlier: 6.546A pdb=" N TRP Y 149 " --> pdb=" O LEU Y 161 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR Y 163 " --> pdb=" O VAL Y 147 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL Y 147 " --> pdb=" O TYR Y 163 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER Y 148 " --> pdb=" O LEU Y 203 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE Y 201 " --> pdb=" O TYR Y 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 2 through 4 removed outlier: 3.686A pdb=" N CYS G 20 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA G 67 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 8 through 10 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 49 removed outlier: 6.643A pdb=" N TRP G 34 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG G 48 " --> pdb=" O MET G 32 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET G 32 " --> pdb=" O ARG G 48 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL G 35 " --> pdb=" O PHE G 93 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN G 37 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL G 91 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 119 through 120 removed outlier: 3.612A pdb=" N CYS J 137 " --> pdb=" O PHE J 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 167 through 168 removed outlier: 6.545A pdb=" N TRP J 149 " --> pdb=" O LEU J 161 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR J 163 " --> pdb=" O VAL J 147 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL J 147 " --> pdb=" O TYR J 163 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER J 148 " --> pdb=" O LEU J 203 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE J 201 " --> pdb=" O TYR J 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 2 through 4 removed outlier: 3.687A pdb=" N CYS I 20 " --> pdb=" O ALA I 77 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA I 67 " --> pdb=" O GLN I 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 8 through 10 Processing sheet with id=AB4, first strand: chain 'I' and resid 42 through 49 removed outlier: 6.644A pdb=" N TRP I 34 " --> pdb=" O ILE I 46 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG I 48 " --> pdb=" O MET I 32 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET I 32 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL I 35 " --> pdb=" O PHE I 93 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN I 37 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL I 91 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 119 through 120 removed outlier: 3.611A pdb=" N CYS K 137 " --> pdb=" O PHE K 185 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 167 through 168 removed outlier: 6.545A pdb=" N TRP K 149 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N TYR K 163 " --> pdb=" O VAL K 147 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL K 147 " --> pdb=" O TYR K 163 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER K 148 " --> pdb=" O LEU K 203 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE K 201 " --> pdb=" O TYR K 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 31 through 33 removed outlier: 3.720A pdb=" N VAL A 40 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 41 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS B 315 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 243 through 244 removed outlier: 5.469A pdb=" N SER B 287 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN B 302 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N MET B 289 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL B 300 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 297 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 59 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLY B 307 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ARG A 49 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA A 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS B 367 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 243 through 244 removed outlier: 5.469A pdb=" N SER B 287 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN B 302 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N MET B 289 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL B 300 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 297 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 59 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLY B 307 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ARG A 49 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA A 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL D 469 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 335 through 336 Processing sheet with id=AC2, first strand: chain 'B' and resid 341 through 345 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 3.907A pdb=" N CYS B 416 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 430 through 434 removed outlier: 7.153A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR B 434 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N CYS B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR B 449 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 466 through 467 removed outlier: 6.595A pdb=" N LEU B 467 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA E 47 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE F 309 " --> pdb=" O ALA E 47 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ARG E 49 " --> pdb=" O GLY F 307 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLY F 307 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 59 " --> pdb=" O LEU F 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 297 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA F 298 " --> pdb=" O SER F 290 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 466 through 467 removed outlier: 6.595A pdb=" N LEU B 467 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS F 367 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 31 through 33 removed outlier: 3.730A pdb=" N VAL C 40 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 41 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS D 315 " --> pdb=" O SER C 41 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 243 through 244 removed outlier: 3.597A pdb=" N SER D 287 " --> pdb=" O THR D 244 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER D 287 " --> pdb=" O GLN D 302 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLN D 302 " --> pdb=" O SER D 287 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N MET D 289 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL D 300 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 297 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 59 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLY D 307 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ARG C 49 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE D 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA C 47 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS D 367 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 243 through 244 removed outlier: 3.597A pdb=" N SER D 287 " --> pdb=" O THR D 244 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER D 287 " --> pdb=" O GLN D 302 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLN D 302 " --> pdb=" O SER D 287 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N MET D 289 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL D 300 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 297 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 59 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLY D 307 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ARG C 49 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE D 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA C 47 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 341 through 345 removed outlier: 3.519A pdb=" N TRP D 341 " --> pdb=" O PHE D 352 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 404 through 407 removed outlier: 3.758A pdb=" N SER D 404 " --> pdb=" O SER D 415 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N CYS D 416 " --> pdb=" O GLY D 438 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 430 through 434 removed outlier: 7.159A pdb=" N ALA D 424 " --> pdb=" O ILE D 432 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR D 434 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N CYS D 422 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR D 449 " --> pdb=" O SER D 425 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 31 through 33 removed outlier: 3.742A pdb=" N VAL E 40 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR E 33 " --> pdb=" O SER E 38 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER E 41 " --> pdb=" O LYS F 315 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS F 315 " --> pdb=" O SER E 41 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 341 through 345 removed outlier: 3.592A pdb=" N TRP F 341 " --> pdb=" O PHE F 352 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 404 through 407 removed outlier: 3.704A pdb=" N SER F 404 " --> pdb=" O SER F 415 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS F 416 " --> pdb=" O GLY F 438 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 430 through 434 removed outlier: 7.146A pdb=" N ALA F 424 " --> pdb=" O ILE F 432 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N THR F 434 " --> pdb=" O CYS F 422 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N CYS F 422 " --> pdb=" O THR F 434 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR F 449 " --> pdb=" O SER F 425 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1425 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: 2.10 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4819 1.34 - 1.46: 3582 1.46 - 1.59: 6936 1.59 - 1.71: 0 1.71 - 1.83: 114 Bond restraints: 15451 Sorted by residual: bond pdb=" C ASP D 310 " pdb=" N THR D 311 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.59e-02 3.96e+03 4.05e+00 bond pdb=" C1 NAG B 800 " pdb=" O5 NAG B 800 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" CB GLU D 236 " pdb=" CG GLU D 236 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.21e+00 bond pdb=" C1 NAG F 800 " pdb=" O5 NAG F 800 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" CG1 ILE D 233 " pdb=" CD1 ILE D 233 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.35e+00 ... (remaining 15446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 20267 2.54 - 5.07: 591 5.07 - 7.61: 49 7.61 - 10.15: 7 10.15 - 12.69: 3 Bond angle restraints: 20917 Sorted by residual: angle pdb=" C ALA B 153 " pdb=" N VAL B 154 " pdb=" CA VAL B 154 " ideal model delta sigma weight residual 120.77 128.68 -7.91 1.31e+00 5.83e-01 3.65e+01 angle pdb=" N ASP B 401 " pdb=" CA ASP B 401 " pdb=" C ASP B 401 " ideal model delta sigma weight residual 107.93 115.36 -7.43 1.65e+00 3.67e-01 2.03e+01 angle pdb=" N THR B 267 " pdb=" CA THR B 267 " pdb=" C THR B 267 " ideal model delta sigma weight residual 110.43 116.07 -5.64 1.31e+00 5.83e-01 1.85e+01 angle pdb=" N LYS F 399 " pdb=" CA LYS F 399 " pdb=" C LYS F 399 " ideal model delta sigma weight residual 113.18 107.60 5.58 1.33e+00 5.65e-01 1.76e+01 angle pdb=" N LYS D 399 " pdb=" CA LYS D 399 " pdb=" C LYS D 399 " ideal model delta sigma weight residual 113.18 107.61 5.57 1.33e+00 5.65e-01 1.75e+01 ... (remaining 20912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 9122 21.29 - 42.58: 316 42.58 - 63.86: 40 63.86 - 85.15: 8 85.15 - 106.44: 8 Dihedral angle restraints: 9494 sinusoidal: 3829 harmonic: 5665 Sorted by residual: dihedral pdb=" CA ASP B 401 " pdb=" C ASP B 401 " pdb=" N VAL B 402 " pdb=" CA VAL B 402 " ideal model delta harmonic sigma weight residual 180.00 138.46 41.54 0 5.00e+00 4.00e-02 6.90e+01 dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 393 " pdb=" CB CYS B 393 " ideal model delta sinusoidal sigma weight residual -86.00 -148.95 62.95 1 1.00e+01 1.00e-02 5.23e+01 dihedral pdb=" CB CYS A 69 " pdb=" SG CYS A 69 " pdb=" SG CYS B 212 " pdb=" CB CYS B 212 " ideal model delta sinusoidal sigma weight residual -86.00 -139.14 53.14 1 1.00e+01 1.00e-02 3.84e+01 ... (remaining 9491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 2439 0.153 - 0.306: 12 0.306 - 0.459: 0 0.459 - 0.612: 0 0.612 - 0.764: 3 Chirality restraints: 2454 Sorted by residual: chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 70 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 70 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 70 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.43e+01 ... (remaining 2451 not shown) Planarity restraints: 2634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 401 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C ASP B 401 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP B 401 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL B 402 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 264 " -0.035 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO B 265 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 265 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 265 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 264 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO D 265 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 265 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 265 " -0.029 5.00e-02 4.00e+02 ... (remaining 2631 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1551 2.74 - 3.28: 14514 3.28 - 3.82: 25191 3.82 - 4.36: 28952 4.36 - 4.90: 48518 Nonbonded interactions: 118726 Sorted by model distance: nonbonded pdb=" O VAL D 482 " pdb=" OH TYR F 198 " model vdw 2.198 3.040 nonbonded pdb=" O ILE B 499 " pdb=" OG SER B 502 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR B 198 " pdb=" O VAL F 482 " model vdw 2.249 3.040 nonbonded pdb=" O VAL B 482 " pdb=" OH TYR D 198 " model vdw 2.253 3.040 nonbonded pdb=" O VAL F 187 " pdb=" OG SER F 190 " model vdw 2.259 3.040 ... (remaining 118721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 97 or resid 601)) selection = chain 'C' selection = (chain 'E' and (resid 26 through 97 or resid 601)) } ncs_group { reference = (chain 'B' and resid 155 through 800) selection = (chain 'D' and (resid 155 through 322 or resid 333 through 800)) selection = (chain 'F' and (resid 155 through 322 or resid 333 through 800)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'X' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.560 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15475 Z= 0.308 Angle : 1.061 19.040 20968 Z= 0.595 Chirality : 0.060 0.764 2454 Planarity : 0.006 0.054 2631 Dihedral : 11.599 106.438 5771 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.29 % Allowed : 4.94 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.06 (0.15), residues: 1915 helix: -3.46 (0.15), residues: 418 sheet: -2.14 (0.20), residues: 469 loop : -2.62 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG B 282 TYR 0.032 0.003 TYR F 250 PHE 0.018 0.003 PHE G 103 TRP 0.019 0.003 TRP Y 206 HIS 0.006 0.002 HIS Y 169 Details of bonding type rmsd covalent geometry : bond 0.00649 (15451) covalent geometry : angle 1.02791 (20917) SS BOND : bond 0.00404 ( 21) SS BOND : angle 1.81579 ( 42) hydrogen bonds : bond 0.29914 ( 520) hydrogen bonds : angle 10.90381 ( 1425) link_NAG-ASN : bond 0.02615 ( 3) link_NAG-ASN : angle 12.35604 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 649 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 200 TYR cc_start: 0.7843 (m-80) cc_final: 0.6648 (m-10) REVERT: Y 216 THR cc_start: 0.6778 (m) cc_final: 0.6169 (m) REVERT: Y 218 LEU cc_start: 0.8141 (mp) cc_final: 0.7925 (mp) REVERT: J 200 TYR cc_start: 0.7868 (m-80) cc_final: 0.6117 (m-80) REVERT: J 202 CYS cc_start: 0.5799 (t) cc_final: 0.5481 (t) REVERT: J 216 THR cc_start: 0.6877 (m) cc_final: 0.6611 (m) REVERT: J 218 LEU cc_start: 0.8271 (mp) cc_final: 0.7490 (mp) REVERT: I 19 SER cc_start: 0.7740 (m) cc_final: 0.7469 (p) REVERT: I 49 LEU cc_start: 0.8052 (tt) cc_final: 0.7836 (tp) REVERT: K 200 TYR cc_start: 0.8298 (m-80) cc_final: 0.7070 (m-10) REVERT: K 218 LEU cc_start: 0.8489 (mp) cc_final: 0.8076 (mp) REVERT: A 33 TYR cc_start: 0.6997 (m-80) cc_final: 0.6737 (m-80) REVERT: B 171 LEU cc_start: 0.8833 (tt) cc_final: 0.8623 (tt) REVERT: B 410 LEU cc_start: 0.7513 (pt) cc_final: 0.6705 (pt) REVERT: C 45 LEU cc_start: 0.8319 (pt) cc_final: 0.7888 (pt) REVERT: C 85 LYS cc_start: 0.8846 (tmmt) cc_final: 0.8183 (tttt) REVERT: D 505 PHE cc_start: 0.8304 (m-80) cc_final: 0.8069 (m-80) REVERT: E 85 LYS cc_start: 0.8943 (tmmt) cc_final: 0.8146 (ttpp) REVERT: E 88 ASN cc_start: 0.7669 (m110) cc_final: 0.7398 (m110) REVERT: F 171 LEU cc_start: 0.8836 (tt) cc_final: 0.8499 (tt) REVERT: F 280 ILE cc_start: 0.8224 (mm) cc_final: 0.7775 (mm) outliers start: 5 outliers final: 0 residues processed: 650 average time/residue: 0.1221 time to fit residues: 109.5842 Evaluate side-chains 305 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.2980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 80 GLN X 99 ASN Y 141 GLN Y 169 HIS ** Y 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 205 HIS J 167 ASN J 169 HIS J 205 HIS I 37 GLN ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 HIS K 205 HIS A 67 ASN A 81 GLN A 98 GLN B 159 HIS B 268 ASN B 496 ASN B 501 GLN C 67 ASN ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 ASN E 81 GLN F 159 HIS F 175 ASN F 227 ASN F 268 ASN F 494 GLN F 496 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.075063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.065297 restraints weight = 90714.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.066678 restraints weight = 54307.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.067574 restraints weight = 36817.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.068224 restraints weight = 27763.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.068623 restraints weight = 22533.982| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15475 Z= 0.147 Angle : 0.768 14.580 20968 Z= 0.391 Chirality : 0.048 0.483 2454 Planarity : 0.005 0.045 2631 Dihedral : 7.749 70.065 2188 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.39 % Allowed : 17.01 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.20 (0.17), residues: 1915 helix: -2.32 (0.20), residues: 457 sheet: -1.64 (0.22), residues: 490 loop : -2.24 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 235 TYR 0.026 0.002 TYR B 391 PHE 0.024 0.002 PHE B 505 TRP 0.020 0.002 TRP K 149 HIS 0.005 0.001 HIS J 205 Details of bonding type rmsd covalent geometry : bond 0.00327 (15451) covalent geometry : angle 0.74508 (20917) SS BOND : bond 0.00500 ( 21) SS BOND : angle 0.91130 ( 42) hydrogen bonds : bond 0.04578 ( 520) hydrogen bonds : angle 7.48191 ( 1425) link_NAG-ASN : bond 0.01772 ( 3) link_NAG-ASN : angle 8.85085 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 376 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 200 TYR cc_start: 0.7244 (m-80) cc_final: 0.6233 (m-80) REVERT: Y 205 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.7964 (t70) REVERT: J 144 ARG cc_start: 0.7076 (mpt90) cc_final: 0.6592 (mmt180) REVERT: J 149 TRP cc_start: 0.5863 (m100) cc_final: 0.5655 (m100) REVERT: J 162 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8596 (tp) REVERT: J 195 GLU cc_start: 0.7738 (pt0) cc_final: 0.7420 (mp0) REVERT: I 25 TYR cc_start: 0.7075 (t80) cc_final: 0.6775 (t80) REVERT: K 200 TYR cc_start: 0.7362 (m-80) cc_final: 0.6620 (m-10) REVERT: K 205 HIS cc_start: 0.8640 (OUTLIER) cc_final: 0.8190 (t70) REVERT: K 218 LEU cc_start: 0.8509 (mp) cc_final: 0.8017 (mp) REVERT: B 280 ILE cc_start: 0.8264 (mm) cc_final: 0.8046 (mt) REVERT: B 400 THR cc_start: 0.6841 (OUTLIER) cc_final: 0.6539 (p) REVERT: C 67 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8187 (m-40) REVERT: C 82 GLU cc_start: 0.7110 (tp30) cc_final: 0.6597 (tp30) REVERT: E 82 GLU cc_start: 0.7371 (tp30) cc_final: 0.6787 (tp30) REVERT: E 88 ASN cc_start: 0.7993 (m110) cc_final: 0.7731 (m110) REVERT: F 280 ILE cc_start: 0.8657 (mm) cc_final: 0.8315 (mt) REVERT: F 486 ASP cc_start: 0.6512 (p0) cc_final: 0.6155 (p0) outliers start: 59 outliers final: 18 residues processed: 415 average time/residue: 0.1101 time to fit residues: 66.4391 Evaluate side-chains 306 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 283 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 205 HIS Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain K residue 205 HIS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 180 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 4 optimal weight: 0.0040 chunk 74 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 99 ASN Y 122 GLN ** Y 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 205 HIS I 37 GLN K 141 GLN K 167 ASN K 205 HIS A 67 ASN B 183 ASN B 228 ASN B 462 GLN B 501 GLN C 67 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 ASN D 284 GLN F 183 ASN ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.071086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.061435 restraints weight = 94995.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.062771 restraints weight = 55017.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.063682 restraints weight = 36682.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.064242 restraints weight = 27468.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.064574 restraints weight = 22479.941| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15475 Z= 0.195 Angle : 0.772 14.655 20968 Z= 0.393 Chirality : 0.048 0.472 2454 Planarity : 0.005 0.054 2631 Dihedral : 6.861 56.385 2188 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.85 % Allowed : 19.08 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.17), residues: 1915 helix: -1.56 (0.22), residues: 451 sheet: -1.19 (0.24), residues: 452 loop : -2.29 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 48 TYR 0.018 0.002 TYR C 33 PHE 0.015 0.002 PHE G 62 TRP 0.015 0.002 TRP I 34 HIS 0.014 0.002 HIS J 205 Details of bonding type rmsd covalent geometry : bond 0.00428 (15451) covalent geometry : angle 0.74924 (20917) SS BOND : bond 0.00283 ( 21) SS BOND : angle 0.88984 ( 42) hydrogen bonds : bond 0.04269 ( 520) hydrogen bonds : angle 7.09570 ( 1425) link_NAG-ASN : bond 0.01817 ( 3) link_NAG-ASN : angle 8.88022 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 302 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 185 PHE cc_start: 0.6762 (m-80) cc_final: 0.6395 (m-10) REVERT: Y 200 TYR cc_start: 0.7386 (m-80) cc_final: 0.6669 (m-80) REVERT: Y 205 HIS cc_start: 0.8496 (OUTLIER) cc_final: 0.8094 (t70) REVERT: J 195 GLU cc_start: 0.7883 (pt0) cc_final: 0.7089 (mp0) REVERT: I 68 LEU cc_start: 0.8362 (tp) cc_final: 0.8089 (tp) REVERT: K 153 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7373 (mtmm) REVERT: K 200 TYR cc_start: 0.7646 (m-80) cc_final: 0.6770 (m-80) REVERT: B 289 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6797 (ptt) REVERT: B 400 THR cc_start: 0.6671 (OUTLIER) cc_final: 0.6351 (p) REVERT: C 82 GLU cc_start: 0.7452 (tp30) cc_final: 0.7188 (tp30) REVERT: E 88 ASN cc_start: 0.7889 (m110) cc_final: 0.7543 (m110) REVERT: F 250 TYR cc_start: 0.7285 (m-10) cc_final: 0.6905 (m-10) REVERT: F 391 TYR cc_start: 0.4792 (t80) cc_final: 0.4531 (t80) outliers start: 67 outliers final: 40 residues processed: 348 average time/residue: 0.0916 time to fit residues: 47.7890 Evaluate side-chains 304 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 260 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 205 HIS Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 367 CYS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 150 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 205 HIS J 205 HIS A 67 ASN B 202 GLN C 67 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 GLN ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.072207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.062661 restraints weight = 93550.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.063996 restraints weight = 54143.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.064881 restraints weight = 36182.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.065453 restraints weight = 27072.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.065794 restraints weight = 22106.452| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15475 Z= 0.137 Angle : 0.729 13.920 20968 Z= 0.363 Chirality : 0.047 0.475 2454 Planarity : 0.004 0.036 2631 Dihedral : 6.165 53.347 2188 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.62 % Allowed : 20.17 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.17), residues: 1915 helix: -1.32 (0.22), residues: 452 sheet: -1.05 (0.24), residues: 459 loop : -2.15 (0.17), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 48 TYR 0.017 0.002 TYR B 391 PHE 0.030 0.002 PHE I 103 TRP 0.027 0.002 TRP I 34 HIS 0.006 0.001 HIS Y 205 Details of bonding type rmsd covalent geometry : bond 0.00304 (15451) covalent geometry : angle 0.70703 (20917) SS BOND : bond 0.00454 ( 21) SS BOND : angle 0.78751 ( 42) hydrogen bonds : bond 0.03723 ( 520) hydrogen bonds : angle 6.67510 ( 1425) link_NAG-ASN : bond 0.01670 ( 3) link_NAG-ASN : angle 8.54077 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 292 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 159 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8449 (mmtt) REVERT: Y 185 PHE cc_start: 0.6842 (m-80) cc_final: 0.6613 (m-10) REVERT: Y 200 TYR cc_start: 0.7433 (m-80) cc_final: 0.6677 (m-80) REVERT: Y 205 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7801 (t70) REVERT: J 149 TRP cc_start: 0.6001 (m100) cc_final: 0.5532 (m100) REVERT: J 159 LYS cc_start: 0.9237 (mttt) cc_final: 0.8734 (mttm) REVERT: J 162 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8688 (tp) REVERT: J 195 GLU cc_start: 0.7941 (pt0) cc_final: 0.7087 (mp0) REVERT: I 68 LEU cc_start: 0.8349 (tp) cc_final: 0.8135 (tp) REVERT: K 149 TRP cc_start: 0.6704 (m100) cc_final: 0.5710 (m-10) REVERT: K 200 TYR cc_start: 0.7525 (m-80) cc_final: 0.6999 (m-10) REVERT: B 400 THR cc_start: 0.6751 (OUTLIER) cc_final: 0.6474 (p) REVERT: C 58 THR cc_start: 0.8011 (m) cc_final: 0.7674 (m) REVERT: E 88 ASN cc_start: 0.7627 (m110) cc_final: 0.7324 (m110) REVERT: F 336 ARG cc_start: 0.6901 (mmm160) cc_final: 0.6523 (mmm160) outliers start: 63 outliers final: 40 residues processed: 336 average time/residue: 0.0869 time to fit residues: 44.1548 Evaluate side-chains 300 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain Y residue 205 HIS Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 367 CYS Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 164 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 184 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 167 ASN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 HIS A 67 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN C 67 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 GLN D 462 GLN ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.068112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.058784 restraints weight = 96957.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.060031 restraints weight = 55717.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.060879 restraints weight = 37192.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.061380 restraints weight = 27770.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.061697 restraints weight = 22871.804| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.6197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15475 Z= 0.262 Angle : 0.827 14.952 20968 Z= 0.425 Chirality : 0.049 0.460 2454 Planarity : 0.005 0.056 2631 Dihedral : 6.669 55.139 2188 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.17 % Allowed : 20.34 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.68 (0.17), residues: 1915 helix: -1.27 (0.22), residues: 446 sheet: -1.29 (0.23), residues: 491 loop : -2.29 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 429 TYR 0.021 0.003 TYR J 200 PHE 0.032 0.002 PHE G 103 TRP 0.055 0.003 TRP G 104 HIS 0.016 0.002 HIS J 205 Details of bonding type rmsd covalent geometry : bond 0.00571 (15451) covalent geometry : angle 0.80441 (20917) SS BOND : bond 0.00329 ( 21) SS BOND : angle 1.36615 ( 42) hydrogen bonds : bond 0.04473 ( 520) hydrogen bonds : angle 7.00612 ( 1425) link_NAG-ASN : bond 0.01753 ( 3) link_NAG-ASN : angle 8.94999 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 251 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 159 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8835 (mmtt) REVERT: Y 185 PHE cc_start: 0.7452 (m-80) cc_final: 0.7044 (m-10) REVERT: Y 200 TYR cc_start: 0.7142 (m-80) cc_final: 0.6211 (m-80) REVERT: Y 205 HIS cc_start: 0.8427 (OUTLIER) cc_final: 0.8116 (t-170) REVERT: I 49 LEU cc_start: 0.7398 (tp) cc_final: 0.7120 (tp) REVERT: I 68 LEU cc_start: 0.8337 (tp) cc_final: 0.8120 (tp) REVERT: K 159 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8603 (mmmt) REVERT: K 200 TYR cc_start: 0.7658 (m-80) cc_final: 0.7007 (m-80) REVERT: K 205 HIS cc_start: 0.8926 (OUTLIER) cc_final: 0.8574 (t70) REVERT: A 68 LYS cc_start: 0.7342 (mmpt) cc_final: 0.6993 (mttm) REVERT: B 173 SER cc_start: 0.9353 (m) cc_final: 0.9124 (p) REVERT: B 289 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7041 (ptt) REVERT: B 370 MET cc_start: 0.8089 (tpt) cc_final: 0.7816 (tpp) REVERT: B 400 THR cc_start: 0.6729 (OUTLIER) cc_final: 0.6423 (p) REVERT: B 410 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7940 (mt) REVERT: C 82 GLU cc_start: 0.7873 (tp30) cc_final: 0.7629 (mm-30) REVERT: D 370 MET cc_start: 0.8178 (mmm) cc_final: 0.7956 (tpp) REVERT: D 408 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7639 (p) REVERT: D 410 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7301 (tp) REVERT: F 289 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7342 (tmm) outliers start: 90 outliers final: 59 residues processed: 318 average time/residue: 0.0885 time to fit residues: 42.5274 Evaluate side-chains 300 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 232 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 187 LEU Chi-restraints excluded: chain Y residue 192 VAL Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain Y residue 205 HIS Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 205 HIS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 40 optimal weight: 8.9990 chunk 75 optimal weight: 0.0470 chunk 84 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 overall best weight: 3.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 205 HIS ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 HIS ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.068733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.059342 restraints weight = 95400.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.060595 restraints weight = 55508.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.061445 restraints weight = 37215.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.061945 restraints weight = 27936.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.062342 restraints weight = 23024.719| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15475 Z= 0.198 Angle : 0.780 14.658 20968 Z= 0.389 Chirality : 0.048 0.459 2454 Planarity : 0.004 0.079 2631 Dihedral : 6.328 53.646 2188 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.06 % Allowed : 21.72 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.17), residues: 1915 helix: -1.12 (0.22), residues: 447 sheet: -1.25 (0.23), residues: 480 loop : -2.27 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 48 TYR 0.019 0.002 TYR J 200 PHE 0.024 0.002 PHE I 103 TRP 0.033 0.002 TRP G 104 HIS 0.010 0.001 HIS J 205 Details of bonding type rmsd covalent geometry : bond 0.00433 (15451) covalent geometry : angle 0.75752 (20917) SS BOND : bond 0.00256 ( 21) SS BOND : angle 1.23965 ( 42) hydrogen bonds : bond 0.04115 ( 520) hydrogen bonds : angle 6.80393 ( 1425) link_NAG-ASN : bond 0.01716 ( 3) link_NAG-ASN : angle 8.71257 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 248 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 159 LYS cc_start: 0.9038 (mmtt) cc_final: 0.8724 (mmtt) REVERT: Y 185 PHE cc_start: 0.7574 (m-80) cc_final: 0.7307 (m-10) REVERT: Y 200 TYR cc_start: 0.6773 (m-80) cc_final: 0.5944 (m-80) REVERT: Y 205 HIS cc_start: 0.8655 (OUTLIER) cc_final: 0.8337 (t70) REVERT: J 159 LYS cc_start: 0.9294 (mttt) cc_final: 0.8912 (mttt) REVERT: J 195 GLU cc_start: 0.8066 (pt0) cc_final: 0.7173 (mp0) REVERT: I 68 LEU cc_start: 0.8217 (tp) cc_final: 0.8001 (tp) REVERT: I 78 TYR cc_start: 0.7637 (m-80) cc_final: 0.7291 (m-80) REVERT: K 159 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8774 (mmmt) REVERT: K 200 TYR cc_start: 0.7384 (m-80) cc_final: 0.6575 (m-80) REVERT: K 205 HIS cc_start: 0.8918 (OUTLIER) cc_final: 0.8568 (t70) REVERT: A 68 LYS cc_start: 0.7534 (mmpt) cc_final: 0.7077 (mttm) REVERT: B 173 SER cc_start: 0.9324 (m) cc_final: 0.9097 (p) REVERT: B 289 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6936 (ptt) REVERT: B 400 THR cc_start: 0.6850 (OUTLIER) cc_final: 0.6558 (p) REVERT: B 410 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7313 (tp) REVERT: C 58 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7826 (m) REVERT: D 410 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7139 (tp) REVERT: F 171 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9042 (tt) REVERT: F 408 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.7989 (p) outliers start: 88 outliers final: 59 residues processed: 315 average time/residue: 0.0871 time to fit residues: 41.9215 Evaluate side-chains 299 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 230 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 192 VAL Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain Y residue 205 HIS Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 205 HIS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 505 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 188 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 HIS ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.067971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.058743 restraints weight = 95459.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.059952 restraints weight = 55378.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.060796 restraints weight = 37339.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.061310 restraints weight = 27894.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.061638 restraints weight = 22845.995| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.6776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15475 Z= 0.227 Angle : 0.819 16.043 20968 Z= 0.411 Chirality : 0.049 0.454 2454 Planarity : 0.004 0.040 2631 Dihedral : 6.472 54.354 2188 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 5.17 % Allowed : 22.41 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.17), residues: 1915 helix: -1.14 (0.22), residues: 446 sheet: -1.34 (0.23), residues: 479 loop : -2.36 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 507 TYR 0.021 0.002 TYR J 200 PHE 0.023 0.002 PHE K 212 TRP 0.069 0.003 TRP G 104 HIS 0.008 0.001 HIS Y 205 Details of bonding type rmsd covalent geometry : bond 0.00500 (15451) covalent geometry : angle 0.79651 (20917) SS BOND : bond 0.00298 ( 21) SS BOND : angle 1.48106 ( 42) hydrogen bonds : bond 0.04257 ( 520) hydrogen bonds : angle 6.95808 ( 1425) link_NAG-ASN : bond 0.01736 ( 3) link_NAG-ASN : angle 8.73555 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 242 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 8 GLU cc_start: 0.5851 (tp30) cc_final: 0.5265 (tp30) REVERT: X 21 LYS cc_start: 0.7783 (tptt) cc_final: 0.7558 (tptp) REVERT: X 53 ASP cc_start: 0.7610 (p0) cc_final: 0.7108 (t0) REVERT: Y 159 LYS cc_start: 0.9101 (mmtt) cc_final: 0.8762 (mmtt) REVERT: Y 200 TYR cc_start: 0.6837 (m-80) cc_final: 0.6065 (m-80) REVERT: J 195 GLU cc_start: 0.8057 (pt0) cc_final: 0.7123 (mp0) REVERT: J 205 HIS cc_start: 0.8627 (OUTLIER) cc_final: 0.8248 (m90) REVERT: I 49 LEU cc_start: 0.7293 (tp) cc_final: 0.7091 (tp) REVERT: I 68 LEU cc_start: 0.8264 (tp) cc_final: 0.8058 (tp) REVERT: K 159 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8855 (mmmt) REVERT: K 205 HIS cc_start: 0.8987 (OUTLIER) cc_final: 0.8608 (t70) REVERT: A 68 LYS cc_start: 0.7719 (mmpt) cc_final: 0.7158 (mttm) REVERT: B 173 SER cc_start: 0.9312 (m) cc_final: 0.9088 (p) REVERT: B 226 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.7839 (pttt) REVERT: B 289 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6744 (ptt) REVERT: B 400 THR cc_start: 0.6806 (OUTLIER) cc_final: 0.6534 (p) REVERT: B 410 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7375 (tp) REVERT: C 58 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7926 (m) REVERT: C 82 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6670 (mm-30) REVERT: D 408 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7427 (p) REVERT: D 410 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7157 (tp) REVERT: F 171 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8997 (tt) outliers start: 90 outliers final: 67 residues processed: 308 average time/residue: 0.0898 time to fit residues: 42.2365 Evaluate side-chains 311 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 233 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 192 VAL Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 201 PHE Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain K residue 205 HIS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 183 ASN Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 505 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 168 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 205 HIS ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 HIS ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.069899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.060516 restraints weight = 94607.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.061783 restraints weight = 55219.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.062657 restraints weight = 37079.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.063154 restraints weight = 27676.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.063561 restraints weight = 22834.242| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.6930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15475 Z= 0.142 Angle : 0.763 16.728 20968 Z= 0.372 Chirality : 0.048 0.464 2454 Planarity : 0.004 0.041 2631 Dihedral : 5.993 53.409 2188 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.48 % Allowed : 23.45 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.18), residues: 1915 helix: -0.96 (0.23), residues: 446 sheet: -1.16 (0.23), residues: 463 loop : -2.28 (0.17), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 507 TYR 0.017 0.002 TYR A 33 PHE 0.018 0.002 PHE K 212 TRP 0.047 0.002 TRP G 104 HIS 0.003 0.001 HIS Y 205 Details of bonding type rmsd covalent geometry : bond 0.00316 (15451) covalent geometry : angle 0.74169 (20917) SS BOND : bond 0.00210 ( 21) SS BOND : angle 1.19220 ( 42) hydrogen bonds : bond 0.03779 ( 520) hydrogen bonds : angle 6.53502 ( 1425) link_NAG-ASN : bond 0.01696 ( 3) link_NAG-ASN : angle 8.39447 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 263 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 53 ASP cc_start: 0.7573 (p0) cc_final: 0.6958 (t0) REVERT: Y 159 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8669 (mmtt) REVERT: J 159 LYS cc_start: 0.9297 (mttt) cc_final: 0.8819 (mttm) REVERT: J 195 GLU cc_start: 0.8107 (pt0) cc_final: 0.7432 (mp0) REVERT: J 205 HIS cc_start: 0.8461 (OUTLIER) cc_final: 0.8003 (m90) REVERT: I 68 LEU cc_start: 0.8142 (tp) cc_final: 0.7899 (tp) REVERT: I 84 LEU cc_start: 0.4850 (mm) cc_final: 0.4403 (mp) REVERT: K 205 HIS cc_start: 0.8841 (OUTLIER) cc_final: 0.8536 (t70) REVERT: A 68 LYS cc_start: 0.7702 (mmpt) cc_final: 0.7156 (mttm) REVERT: B 173 SER cc_start: 0.9294 (m) cc_final: 0.9071 (p) REVERT: B 226 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.7761 (pmtt) REVERT: B 408 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7697 (p) REVERT: C 49 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7168 (tmm-80) REVERT: C 58 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7734 (m) REVERT: C 81 GLN cc_start: 0.7455 (mm110) cc_final: 0.7248 (mm110) REVERT: C 82 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6916 (mm-30) REVERT: D 408 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7439 (p) REVERT: D 410 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7141 (tp) REVERT: F 171 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9057 (tt) REVERT: F 336 ARG cc_start: 0.6858 (mmm160) cc_final: 0.6192 (mmm160) REVERT: F 408 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7741 (p) outliers start: 78 outliers final: 50 residues processed: 320 average time/residue: 0.0971 time to fit residues: 47.0737 Evaluate side-chains 298 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 238 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 192 VAL Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain Y residue 205 HIS Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 205 HIS Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 96 ARG Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 205 HIS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 83 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 48 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 151 GLN ** J 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.071619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.062235 restraints weight = 95009.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.063545 restraints weight = 55195.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.064353 restraints weight = 36949.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.064955 restraints weight = 27928.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.065360 restraints weight = 22660.471| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.7128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15475 Z= 0.128 Angle : 0.777 17.417 20968 Z= 0.375 Chirality : 0.048 0.463 2454 Planarity : 0.004 0.060 2631 Dihedral : 5.628 53.076 2188 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.16 % Allowed : 25.17 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.18), residues: 1915 helix: -0.99 (0.23), residues: 451 sheet: -1.06 (0.23), residues: 498 loop : -2.01 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 507 TYR 0.016 0.001 TYR G 78 PHE 0.019 0.002 PHE X 103 TRP 0.084 0.002 TRP G 104 HIS 0.018 0.002 HIS Y 205 Details of bonding type rmsd covalent geometry : bond 0.00282 (15451) covalent geometry : angle 0.75850 (20917) SS BOND : bond 0.00160 ( 21) SS BOND : angle 1.00789 ( 42) hydrogen bonds : bond 0.03524 ( 520) hydrogen bonds : angle 6.30254 ( 1425) link_NAG-ASN : bond 0.01640 ( 3) link_NAG-ASN : angle 8.09286 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 270 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 29 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7320 (t0) REVERT: X 53 ASP cc_start: 0.7506 (p0) cc_final: 0.6834 (t0) REVERT: Y 149 TRP cc_start: 0.4913 (m-10) cc_final: 0.4358 (m-10) REVERT: Y 159 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8656 (mmtt) REVERT: G 43 LEU cc_start: 0.8370 (tt) cc_final: 0.8056 (pt) REVERT: J 195 GLU cc_start: 0.8129 (pt0) cc_final: 0.7592 (mp0) REVERT: I 68 LEU cc_start: 0.8169 (tp) cc_final: 0.7942 (tp) REVERT: I 84 LEU cc_start: 0.5169 (mm) cc_final: 0.4876 (mm) REVERT: K 159 LYS cc_start: 0.8853 (mptt) cc_final: 0.8645 (mmmt) REVERT: A 68 LYS cc_start: 0.7700 (mmpt) cc_final: 0.7142 (mttm) REVERT: B 226 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.7788 (pmtt) REVERT: B 370 MET cc_start: 0.8303 (tpt) cc_final: 0.8024 (tpp) REVERT: B 408 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7549 (p) REVERT: B 410 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7354 (tp) REVERT: C 49 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7018 (tmm-80) REVERT: C 58 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7742 (m) REVERT: D 171 LEU cc_start: 0.9136 (mp) cc_final: 0.8791 (tt) REVERT: D 408 THR cc_start: 0.7804 (OUTLIER) cc_final: 0.7480 (p) REVERT: D 410 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7184 (tp) REVERT: F 171 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9106 (tt) REVERT: F 336 ARG cc_start: 0.6645 (mmm160) cc_final: 0.5989 (mmm160) REVERT: F 408 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7617 (p) outliers start: 55 outliers final: 36 residues processed: 306 average time/residue: 0.1091 time to fit residues: 50.5780 Evaluate side-chains 289 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 192 VAL Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain J residue 151 GLN Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 73 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.070968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.061570 restraints weight = 97343.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.062876 restraints weight = 56756.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.063746 restraints weight = 37986.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.064331 restraints weight = 28228.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.064661 restraints weight = 23027.225| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.7176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.233 15475 Z= 0.257 Angle : 0.994 59.197 20968 Z= 0.518 Chirality : 0.052 0.513 2454 Planarity : 0.004 0.060 2631 Dihedral : 5.651 53.130 2188 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.10 % Allowed : 26.26 % Favored : 70.63 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.18), residues: 1915 helix: -1.00 (0.23), residues: 451 sheet: -1.06 (0.23), residues: 503 loop : -2.03 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 48 TYR 0.014 0.002 TYR B 441 PHE 0.020 0.002 PHE X 103 TRP 0.072 0.003 TRP G 104 HIS 0.013 0.002 HIS J 205 Details of bonding type rmsd covalent geometry : bond 0.00587 (15451) covalent geometry : angle 0.97990 (20917) SS BOND : bond 0.00166 ( 21) SS BOND : angle 1.03870 ( 42) hydrogen bonds : bond 0.03605 ( 520) hydrogen bonds : angle 6.30106 ( 1425) link_NAG-ASN : bond 0.01652 ( 3) link_NAG-ASN : angle 8.17987 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 29 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.7345 (t0) REVERT: X 53 ASP cc_start: 0.7572 (p0) cc_final: 0.6877 (t0) REVERT: Y 159 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8677 (mmtt) REVERT: G 43 LEU cc_start: 0.8408 (tt) cc_final: 0.8104 (pt) REVERT: J 195 GLU cc_start: 0.8219 (pt0) cc_final: 0.7615 (mp0) REVERT: I 68 LEU cc_start: 0.8103 (tp) cc_final: 0.7898 (tp) REVERT: I 84 LEU cc_start: 0.5304 (mm) cc_final: 0.4970 (mp) REVERT: K 159 LYS cc_start: 0.8891 (mptt) cc_final: 0.8647 (mmmt) REVERT: A 68 LYS cc_start: 0.7696 (mmpt) cc_final: 0.7094 (mttm) REVERT: B 226 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7762 (pmtt) REVERT: B 370 MET cc_start: 0.8311 (tpt) cc_final: 0.8032 (tpp) REVERT: B 410 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7403 (tp) REVERT: C 58 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7768 (m) REVERT: D 171 LEU cc_start: 0.9104 (mp) cc_final: 0.8810 (tt) REVERT: D 408 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7491 (p) REVERT: D 410 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7205 (tp) REVERT: F 171 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9102 (tt) REVERT: F 336 ARG cc_start: 0.6750 (mmm160) cc_final: 0.6119 (mmm160) REVERT: F 408 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7618 (p) outliers start: 54 outliers final: 43 residues processed: 278 average time/residue: 0.1049 time to fit residues: 44.5957 Evaluate side-chains 291 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 29 ASN Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 192 VAL Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain J residue 153 LYS Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 202 CYS Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 205 HIS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 250 TYR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 90 optimal weight: 0.3980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** 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 = 0.3776 r_free = 0.3776 target = 0.070922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.061618 restraints weight = 93184.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.062896 restraints weight = 55024.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.063748 restraints weight = 37076.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.064340 restraints weight = 27838.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.064678 restraints weight = 22618.019| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.7174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.233 15475 Z= 0.257 Angle : 0.994 59.197 20968 Z= 0.518 Chirality : 0.052 0.513 2454 Planarity : 0.004 0.060 2631 Dihedral : 5.651 53.130 2188 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.93 % Allowed : 26.55 % Favored : 70.52 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.18), residues: 1915 helix: -1.00 (0.23), residues: 451 sheet: -1.06 (0.23), residues: 503 loop : -2.03 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 48 TYR 0.014 0.002 TYR B 441 PHE 0.020 0.002 PHE X 103 TRP 0.072 0.003 TRP G 104 HIS 0.013 0.002 HIS J 205 Details of bonding type rmsd covalent geometry : bond 0.00587 (15451) covalent geometry : angle 0.97990 (20917) SS BOND : bond 0.00166 ( 21) SS BOND : angle 1.03870 ( 42) hydrogen bonds : bond 0.03605 ( 520) hydrogen bonds : angle 6.30106 ( 1425) link_NAG-ASN : bond 0.01652 ( 3) link_NAG-ASN : angle 8.17987 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2419.34 seconds wall clock time: 42 minutes 47.68 seconds (2567.68 seconds total)