Starting phenix.real_space_refine on Wed Mar 4 00:11:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyh_26179/03_2026/7tyh_26179.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyh_26179/03_2026/7tyh_26179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tyh_26179/03_2026/7tyh_26179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyh_26179/03_2026/7tyh_26179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tyh_26179/03_2026/7tyh_26179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyh_26179/03_2026/7tyh_26179.map" } resolution = 3.3 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 68 5.16 5 C 6015 2.51 5 N 1663 2.21 5 O 1746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9492 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2598 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 413 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 514 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 414 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ASN:plan1': 4, 'TYR:plan': 3, 'GLU:plan': 6, 'GLN:plan1': 3, 'PHE:plan': 7, 'ASP:plan': 6, 'TRP:plan': 3, 'ARG:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 186 Chain: "P" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 238 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2867 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 17, 'TRANS': 351} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 2, 'GLU:plan': 5, 'TRP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 122 Time building chain proxies: 2.28, per 1000 atoms: 0.24 Number of scatterers: 9492 At special positions: 0 Unit cell: (89.88, 102.72, 156.648, 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 68 16.00 O 1746 8.00 N 1663 7.00 C 6015 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.01 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 1 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 381.2 milliseconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 12 sheets defined 40.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 4.162A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 27 " --> pdb=" O ASN A 23 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.537A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL A 57 " --> pdb=" O ASN A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 53 through 57' Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.689A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 239' Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.729A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.843A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 removed outlier: 3.960A pdb=" N ASP A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.248A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.639A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.518A pdb=" N ARG B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 22 removed outlier: 3.821A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 34 through 44 removed outlier: 3.588A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 77 removed outlier: 3.608A pdb=" N GLN E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE E 67 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN E 70 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS E 73 " --> pdb=" O TRP E 69 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.551A pdb=" N TYR E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU E 96 " --> pdb=" O PRO E 92 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG E 97 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP E 98 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 100 " --> pdb=" O LEU E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 127 removed outlier: 3.602A pdb=" N ARG E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS E 127 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 156 removed outlier: 3.531A pdb=" N ALA E 152 " --> pdb=" O ALA E 148 " (cutoff:3.500A) Proline residue: E 153 - end of helix Processing helix chain 'E' and resid 157 through 166 removed outlier: 3.551A pdb=" N LEU E 163 " --> pdb=" O PHE E 159 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 165 " --> pdb=" O ILE E 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 22 removed outlier: 3.659A pdb=" N ASN P 17 " --> pdb=" O THR P 13 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE P 19 " --> pdb=" O ASP P 15 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS P 20 " --> pdb=" O PHE P 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 62 removed outlier: 3.753A pdb=" N ASP R 50 " --> pdb=" O LYS R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 removed outlier: 3.925A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 162 removed outlier: 3.572A pdb=" N LYS R 143 " --> pdb=" O PRO R 139 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU R 148 " --> pdb=" O ASN R 144 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER R 159 " --> pdb=" O GLY R 155 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE R 160 " --> pdb=" O HIS R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 171 removed outlier: 4.246A pdb=" N PHE R 170 " --> pdb=" O SER R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.720A pdb=" N ILE R 199 " --> pdb=" O SER R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 214 removed outlier: 3.796A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 246 removed outlier: 3.991A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU R 244 " --> pdb=" O GLU R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 268 removed outlier: 3.584A pdb=" N TRP R 267 " --> pdb=" O TYR R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 284 removed outlier: 3.539A pdb=" N VAL R 283 " --> pdb=" O ILE R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 315 Proline residue: R 304 - end of helix removed outlier: 3.789A pdb=" N VAL R 310 " --> pdb=" O MET R 306 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL R 311 " --> pdb=" O ALA R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 329 Processing helix chain 'R' and resid 333 through 338 removed outlier: 3.941A pdb=" N TYR R 338 " --> pdb=" O GLU R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 344 removed outlier: 3.798A pdb=" N LYS R 343 " --> pdb=" O LEU R 339 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 365 through 382 removed outlier: 3.797A pdb=" N GLY R 369 " --> pdb=" O ASN R 365 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE R 371 " --> pdb=" O MET R 367 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR R 374 " --> pdb=" O LYS R 370 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS R 377 " --> pdb=" O ASP R 373 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER R 378 " --> pdb=" O TYR R 374 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU R 379 " --> pdb=" O VAL R 375 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 389 Processing helix chain 'R' and resid 395 through 400 Processing helix chain 'R' and resid 400 through 405 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213 removed outlier: 3.539A pdb=" N PHE A 222 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.927A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.919A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.368A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.959A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.155A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.679A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 275 removed outlier: 3.553A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.575A pdb=" N VAL N 12 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 17 through 19 Processing sheet with id=AB3, first strand: chain 'R' and resid 75 through 76 removed outlier: 3.533A pdb=" N THR R 75 " --> pdb=" O TRP R 82 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1038 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: 1.63 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1556 1.31 - 1.44: 2703 1.44 - 1.56: 5345 1.56 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 9699 Sorted by residual: bond pdb=" C PRO N 100 " pdb=" O PRO N 100 " ideal model delta sigma weight residual 1.237 1.189 0.049 1.26e-02 6.30e+03 1.49e+01 bond pdb=" N ARG N 98 " pdb=" CA ARG N 98 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.21e-02 6.83e+03 1.36e+01 bond pdb=" N ASP N 106 " pdb=" CA ASP N 106 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.22e-02 6.72e+03 1.24e+01 bond pdb=" N ILE A 276 " pdb=" CA ILE A 276 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.65e+00 bond pdb=" N CYS P 7 " pdb=" CA CYS P 7 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.18e-02 7.18e+03 9.22e+00 ... (remaining 9694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 12985 2.36 - 4.72: 174 4.72 - 7.07: 15 7.07 - 9.43: 2 9.43 - 11.79: 1 Bond angle restraints: 13177 Sorted by residual: angle pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 112.00 100.21 11.79 1.40e+00 5.10e-01 7.09e+01 angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 111.77 120.11 -8.34 1.67e+00 3.59e-01 2.49e+01 angle pdb=" CA PRO N 102 " pdb=" C PRO N 102 " pdb=" O PRO N 102 " ideal model delta sigma weight residual 122.13 116.49 5.64 1.23e+00 6.61e-01 2.10e+01 angle pdb=" CA VAL N 110 " pdb=" C VAL N 110 " pdb=" O VAL N 110 " ideal model delta sigma weight residual 120.85 116.37 4.48 1.06e+00 8.90e-01 1.78e+01 angle pdb=" CA PRO N 102 " pdb=" C PRO N 102 " pdb=" N PHE N 103 " ideal model delta sigma weight residual 114.58 119.39 -4.81 1.16e+00 7.43e-01 1.72e+01 ... (remaining 13172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5337 17.98 - 35.97: 336 35.97 - 53.95: 58 53.95 - 71.93: 12 71.93 - 89.91: 6 Dihedral angle restraints: 5749 sinusoidal: 2117 harmonic: 3632 Sorted by residual: dihedral pdb=" CB CYS P 1 " pdb=" SG CYS P 1 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 154.15 -61.15 1 1.00e+01 1.00e-02 4.97e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -127.86 41.86 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CA ASP N 106 " pdb=" CB ASP N 106 " pdb=" CG ASP N 106 " pdb=" OD1 ASP N 106 " ideal model delta sinusoidal sigma weight residual -30.00 -87.44 57.44 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 5746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1085 0.041 - 0.081: 274 0.081 - 0.122: 104 0.122 - 0.163: 14 0.163 - 0.204: 5 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" C PRO P 32 " pdb=" CB PRO P 32 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA MET P 8 " pdb=" N MET P 8 " pdb=" C MET P 8 " pdb=" CB MET P 8 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA LEU P 4 " pdb=" N LEU P 4 " pdb=" C LEU P 4 " pdb=" CB LEU P 4 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 1479 not shown) Planarity restraints: 1698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA P 31 " -0.117 5.00e-02 4.00e+02 1.67e-01 4.47e+01 pdb=" N PRO P 32 " 0.289 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO N 100 " -0.009 2.00e-02 2.50e+03 1.98e-02 3.90e+00 pdb=" C PRO N 100 " 0.034 2.00e-02 2.50e+03 pdb=" O PRO N 100 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA N 101 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 234 " 0.018 2.00e-02 2.50e+03 1.19e-02 3.54e+00 pdb=" CG TRP A 234 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 234 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 234 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 234 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 234 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 234 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 234 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 234 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 234 " -0.001 2.00e-02 2.50e+03 ... (remaining 1695 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2607 2.80 - 3.32: 8568 3.32 - 3.85: 15089 3.85 - 4.37: 18611 4.37 - 4.90: 31274 Nonbonded interactions: 76149 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.306 3.040 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.315 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.321 3.040 nonbonded pdb=" O ALA A 48 " pdb=" OG SER A 51 " model vdw 2.328 3.040 ... (remaining 76144 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.330 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 9708 Z= 0.247 Angle : 0.607 11.790 13193 Z= 0.408 Chirality : 0.043 0.204 1482 Planarity : 0.005 0.167 1698 Dihedral : 12.285 89.913 3375 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.05 % Allowed : 7.96 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -4.28 (0.19), residues: 1226 helix: -3.18 (0.18), residues: 442 sheet: -3.15 (0.31), residues: 197 loop : -2.32 (0.22), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 232 TYR 0.021 0.001 TYR N 115 PHE 0.024 0.001 PHE N 108 TRP 0.032 0.001 TRP A 234 HIS 0.002 0.000 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9699) covalent geometry : angle 0.60539 (13177) SS BOND : bond 0.00581 ( 8) SS BOND : angle 1.35222 ( 16) hydrogen bonds : bond 0.30188 ( 357) hydrogen bonds : angle 10.11470 ( 1038) Misc. bond : bond 0.10690 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: R 230 MET cc_start: 0.7126 (ttp) cc_final: 0.6374 (ttm) REVERT: R 255 GLU cc_start: 0.3382 (mt-10) cc_final: 0.3136 (tt0) REVERT: R 340 LYS cc_start: 0.7577 (mmmm) cc_final: 0.7312 (mmtm) outliers start: 10 outliers final: 7 residues processed: 200 average time/residue: 0.1107 time to fit residues: 30.2344 Evaluate side-chains 152 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain R residue 349 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.0370 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 230 ASN G 18 GLN N 31 ASN E 124 HIS P 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.190677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.158478 restraints weight = 11148.459| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.01 r_work: 0.3712 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9708 Z= 0.115 Angle : 0.492 6.126 13193 Z= 0.262 Chirality : 0.041 0.151 1482 Planarity : 0.004 0.053 1698 Dihedral : 4.424 59.272 1356 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.51 % Allowed : 11.62 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.91 (0.21), residues: 1226 helix: -1.48 (0.22), residues: 472 sheet: -2.69 (0.32), residues: 204 loop : -1.89 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 19 TYR 0.017 0.001 TYR N 80 PHE 0.013 0.001 PHE N 108 TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9699) covalent geometry : angle 0.49116 (13177) SS BOND : bond 0.00262 ( 8) SS BOND : angle 0.87415 ( 16) hydrogen bonds : bond 0.03964 ( 357) hydrogen bonds : angle 5.26011 ( 1038) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.374 Fit side-chains REVERT: A 280 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7570 (ptmt) REVERT: B 215 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7787 (pm20) REVERT: B 264 TYR cc_start: 0.7580 (m-80) cc_final: 0.7027 (m-80) REVERT: R 230 MET cc_start: 0.7129 (ttp) cc_final: 0.6604 (ttm) outliers start: 24 outliers final: 14 residues processed: 192 average time/residue: 0.1048 time to fit residues: 27.7697 Evaluate side-chains 157 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 105 optimal weight: 0.0770 chunk 41 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 12 optimal weight: 0.0570 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN R 144 ASN R 377 HIS R 405 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.190980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.159081 restraints weight = 11072.512| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.01 r_work: 0.3728 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9708 Z= 0.096 Angle : 0.466 7.092 13193 Z= 0.245 Chirality : 0.040 0.152 1482 Planarity : 0.003 0.049 1698 Dihedral : 3.946 58.833 1353 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.14 % Allowed : 14.03 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.12 (0.22), residues: 1226 helix: -0.57 (0.23), residues: 474 sheet: -2.42 (0.32), residues: 202 loop : -1.63 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 38 TYR 0.015 0.001 TYR P 12 PHE 0.018 0.001 PHE R 161 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 9699) covalent geometry : angle 0.46514 (13177) SS BOND : bond 0.00254 ( 8) SS BOND : angle 1.03385 ( 16) hydrogen bonds : bond 0.03268 ( 357) hydrogen bonds : angle 4.60643 ( 1038) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.382 Fit side-chains REVERT: A 209 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7355 (mt-10) REVERT: B 264 TYR cc_start: 0.7536 (m-80) cc_final: 0.7043 (m-80) REVERT: N 108 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: P 8 MET cc_start: 0.7055 (tpt) cc_final: 0.6415 (ttm) REVERT: R 213 ARG cc_start: 0.6696 (mtp85) cc_final: 0.6435 (mtp180) REVERT: R 230 MET cc_start: 0.7122 (ttp) cc_final: 0.6648 (ttm) REVERT: R 394 CYS cc_start: 0.6760 (m) cc_final: 0.6321 (t) outliers start: 30 outliers final: 17 residues processed: 174 average time/residue: 0.1009 time to fit residues: 24.6623 Evaluate side-chains 162 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 73 optimal weight: 10.0000 chunk 80 optimal weight: 0.0270 chunk 113 optimal weight: 0.3980 chunk 77 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 0.0070 chunk 31 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 109 optimal weight: 0.1980 chunk 104 optimal weight: 3.9990 overall best weight: 0.2056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 295 ASN P 17 ASN R 144 ASN R 383 GLN R 405 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.193962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.162262 restraints weight = 11195.495| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.01 r_work: 0.3755 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9708 Z= 0.081 Angle : 0.441 7.203 13193 Z= 0.232 Chirality : 0.039 0.145 1482 Planarity : 0.003 0.042 1698 Dihedral : 3.723 56.708 1351 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.62 % Allowed : 15.60 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.47 (0.23), residues: 1226 helix: 0.13 (0.24), residues: 478 sheet: -2.13 (0.33), residues: 200 loop : -1.43 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 38 TYR 0.013 0.001 TYR P 12 PHE 0.022 0.001 PHE R 359 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00180 ( 9699) covalent geometry : angle 0.44010 (13177) SS BOND : bond 0.00479 ( 8) SS BOND : angle 0.76176 ( 16) hydrogen bonds : bond 0.02723 ( 357) hydrogen bonds : angle 4.19099 ( 1038) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.311 Fit side-chains REVERT: A 209 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7138 (mt-10) REVERT: B 153 ASP cc_start: 0.8146 (p0) cc_final: 0.7895 (p0) REVERT: B 264 TYR cc_start: 0.7431 (m-80) cc_final: 0.6943 (m-80) REVERT: P 8 MET cc_start: 0.7017 (tpt) cc_final: 0.6466 (ttm) REVERT: R 47 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7783 (mtpt) REVERT: R 213 ARG cc_start: 0.6665 (mtp85) cc_final: 0.6420 (mtp180) REVERT: R 230 MET cc_start: 0.7034 (ttp) cc_final: 0.6695 (ttm) REVERT: R 306 MET cc_start: 0.8610 (mmm) cc_final: 0.8246 (tpt) REVERT: R 394 CYS cc_start: 0.6669 (m) cc_final: 0.6249 (t) outliers start: 25 outliers final: 20 residues processed: 182 average time/residue: 0.0902 time to fit residues: 23.4445 Evaluate side-chains 172 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 252 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 144 ASN R 233 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.186022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.153549 restraints weight = 11199.342| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.96 r_work: 0.3593 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9708 Z= 0.201 Angle : 0.561 7.640 13193 Z= 0.296 Chirality : 0.044 0.164 1482 Planarity : 0.004 0.046 1698 Dihedral : 4.457 58.315 1351 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.98 % Allowed : 16.54 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.61 (0.23), residues: 1226 helix: -0.02 (0.24), residues: 475 sheet: -2.24 (0.33), residues: 205 loop : -1.43 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.015 0.002 TYR P 12 PHE 0.025 0.002 PHE R 161 TRP 0.015 0.002 TRP B 211 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 9699) covalent geometry : angle 0.56020 (13177) SS BOND : bond 0.00279 ( 8) SS BOND : angle 1.12891 ( 16) hydrogen bonds : bond 0.03511 ( 357) hydrogen bonds : angle 4.65994 ( 1038) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.377 Fit side-chains REVERT: A 35 GLN cc_start: 0.7961 (tp40) cc_final: 0.7701 (mm110) REVERT: A 209 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 270 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8606 (mp) REVERT: A 344 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7111 (mm-30) REVERT: B 264 TYR cc_start: 0.7751 (m-80) cc_final: 0.7208 (m-80) REVERT: N 108 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: P 8 MET cc_start: 0.7077 (tpt) cc_final: 0.6548 (ttm) REVERT: R 213 ARG cc_start: 0.6739 (mtp85) cc_final: 0.6451 (mtp180) REVERT: R 230 MET cc_start: 0.7052 (ttp) cc_final: 0.6660 (ttm) outliers start: 38 outliers final: 26 residues processed: 169 average time/residue: 0.0913 time to fit residues: 21.9873 Evaluate side-chains 158 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 89 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN R 93 GLN R 144 ASN R 233 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.183599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.152188 restraints weight = 11179.015| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.90 r_work: 0.3645 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9708 Z= 0.134 Angle : 0.496 7.102 13193 Z= 0.262 Chirality : 0.042 0.159 1482 Planarity : 0.003 0.046 1698 Dihedral : 4.264 58.140 1351 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.56 % Allowed : 17.17 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.36 (0.23), residues: 1226 helix: 0.26 (0.25), residues: 469 sheet: -2.21 (0.33), residues: 205 loop : -1.32 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.015 0.001 TYR P 12 PHE 0.025 0.001 PHE R 359 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9699) covalent geometry : angle 0.49553 (13177) SS BOND : bond 0.00148 ( 8) SS BOND : angle 0.83640 ( 16) hydrogen bonds : bond 0.03074 ( 357) hydrogen bonds : angle 4.43250 ( 1038) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.380 Fit side-chains REVERT: A 35 GLN cc_start: 0.7911 (tp40) cc_final: 0.7633 (mm110) REVERT: A 209 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 390 GLN cc_start: 0.7407 (mm-40) cc_final: 0.7172 (mm-40) REVERT: B 76 ASP cc_start: 0.8917 (p0) cc_final: 0.8625 (p0) REVERT: B 264 TYR cc_start: 0.7531 (m-80) cc_final: 0.6951 (m-80) REVERT: N 108 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7793 (m-80) REVERT: P 8 MET cc_start: 0.6792 (tpt) cc_final: 0.6266 (ttm) REVERT: R 213 ARG cc_start: 0.6630 (mtp85) cc_final: 0.6381 (mtp180) REVERT: R 230 MET cc_start: 0.7020 (ttp) cc_final: 0.6613 (ttm) outliers start: 34 outliers final: 28 residues processed: 168 average time/residue: 0.0928 time to fit residues: 22.2640 Evaluate side-chains 164 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 13 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN R 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.187153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.156038 restraints weight = 11137.758| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.78 r_work: 0.3688 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9708 Z= 0.095 Angle : 0.467 6.789 13193 Z= 0.247 Chirality : 0.041 0.242 1482 Planarity : 0.003 0.044 1698 Dihedral : 3.976 56.363 1351 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.83 % Allowed : 18.43 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.14 (0.23), residues: 1226 helix: 0.51 (0.25), residues: 479 sheet: -2.16 (0.33), residues: 203 loop : -1.26 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.014 0.001 TYR P 12 PHE 0.026 0.001 PHE R 161 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 9699) covalent geometry : angle 0.46642 (13177) SS BOND : bond 0.00097 ( 8) SS BOND : angle 0.66886 ( 16) hydrogen bonds : bond 0.02796 ( 357) hydrogen bonds : angle 4.25857 ( 1038) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.305 Fit side-chains REVERT: A 209 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7534 (mt-10) REVERT: B 264 TYR cc_start: 0.7504 (m-80) cc_final: 0.6927 (m-80) REVERT: P 8 MET cc_start: 0.6728 (tpt) cc_final: 0.6103 (ttm) REVERT: R 230 MET cc_start: 0.6939 (ttp) cc_final: 0.6604 (ttm) REVERT: R 327 MET cc_start: 0.7472 (mtm) cc_final: 0.7199 (mtm) REVERT: R 376 MET cc_start: 0.7992 (mmm) cc_final: 0.7602 (tpp) outliers start: 27 outliers final: 25 residues processed: 166 average time/residue: 0.0821 time to fit residues: 19.5720 Evaluate side-chains 165 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 59 optimal weight: 0.0050 chunk 4 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 96 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.184781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152677 restraints weight = 11149.031| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.92 r_work: 0.3648 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9708 Z= 0.126 Angle : 0.495 8.446 13193 Z= 0.262 Chirality : 0.042 0.297 1482 Planarity : 0.003 0.044 1698 Dihedral : 4.132 56.427 1351 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.25 % Allowed : 19.06 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.00 (0.24), residues: 1226 helix: 0.64 (0.25), residues: 473 sheet: -2.08 (0.33), residues: 202 loop : -1.18 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 38 TYR 0.014 0.001 TYR P 12 PHE 0.025 0.001 PHE R 161 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9699) covalent geometry : angle 0.49470 (13177) SS BOND : bond 0.00133 ( 8) SS BOND : angle 0.74499 ( 16) hydrogen bonds : bond 0.02959 ( 357) hydrogen bonds : angle 4.33217 ( 1038) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7627 (mm110) REVERT: B 226 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7306 (mt-10) REVERT: B 264 TYR cc_start: 0.7618 (m-80) cc_final: 0.7076 (m-80) REVERT: P 8 MET cc_start: 0.6792 (tpt) cc_final: 0.6284 (ttm) REVERT: R 230 MET cc_start: 0.6983 (ttp) cc_final: 0.6566 (ttm) REVERT: R 376 MET cc_start: 0.8130 (mmm) cc_final: 0.7776 (tpp) outliers start: 31 outliers final: 30 residues processed: 158 average time/residue: 0.0827 time to fit residues: 19.3274 Evaluate side-chains 162 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 36 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 22 optimal weight: 0.3980 chunk 116 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 91 optimal weight: 40.0000 chunk 75 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 ASN R 156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.187511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153949 restraints weight = 11193.680| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.09 r_work: 0.3659 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9708 Z= 0.104 Angle : 0.484 8.658 13193 Z= 0.255 Chirality : 0.041 0.277 1482 Planarity : 0.003 0.044 1698 Dihedral : 4.014 55.731 1351 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.14 % Allowed : 19.37 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.24), residues: 1226 helix: 0.74 (0.25), residues: 478 sheet: -2.06 (0.33), residues: 203 loop : -1.14 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.013 0.001 TYR P 12 PHE 0.020 0.001 PHE R 359 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.000 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9699) covalent geometry : angle 0.48420 (13177) SS BOND : bond 0.00091 ( 8) SS BOND : angle 0.65412 ( 16) hydrogen bonds : bond 0.02824 ( 357) hydrogen bonds : angle 4.25395 ( 1038) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7292 (mt-10) REVERT: B 264 TYR cc_start: 0.7506 (m-80) cc_final: 0.6945 (m-80) REVERT: N 47 TRP cc_start: 0.8914 (t60) cc_final: 0.8665 (t60) REVERT: P 8 MET cc_start: 0.6703 (tpt) cc_final: 0.6084 (ttm) REVERT: R 230 MET cc_start: 0.6908 (ttp) cc_final: 0.6580 (ttm) REVERT: R 306 MET cc_start: 0.8347 (mmm) cc_final: 0.8041 (tpt) REVERT: R 376 MET cc_start: 0.8136 (mmm) cc_final: 0.7868 (tpp) outliers start: 30 outliers final: 27 residues processed: 160 average time/residue: 0.0845 time to fit residues: 19.9867 Evaluate side-chains 158 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9980 chunk 22 optimal weight: 0.0050 chunk 104 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 110 optimal weight: 0.0870 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.5772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.188372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.155337 restraints weight = 11162.836| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.04 r_work: 0.3674 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 9708 Z= 0.099 Angle : 0.481 8.752 13193 Z= 0.253 Chirality : 0.041 0.253 1482 Planarity : 0.003 0.044 1698 Dihedral : 3.932 54.963 1351 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.72 % Allowed : 19.79 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.24), residues: 1226 helix: 0.87 (0.25), residues: 480 sheet: -1.98 (0.33), residues: 210 loop : -1.12 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.013 0.001 TYR P 12 PHE 0.024 0.001 PHE R 359 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.000 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9699) covalent geometry : angle 0.48039 (13177) SS BOND : bond 0.00086 ( 8) SS BOND : angle 0.60830 ( 16) hydrogen bonds : bond 0.02784 ( 357) hydrogen bonds : angle 4.19008 ( 1038) Misc. bond : bond 0.00001 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7254 (mt-10) REVERT: B 264 TYR cc_start: 0.7461 (m-80) cc_final: 0.6868 (m-80) REVERT: N 47 TRP cc_start: 0.8891 (t60) cc_final: 0.8654 (t60) REVERT: N 74 ASN cc_start: 0.6209 (m-40) cc_final: 0.5606 (t0) REVERT: P 8 MET cc_start: 0.6632 (tpt) cc_final: 0.6046 (ttm) REVERT: R 230 MET cc_start: 0.6806 (ttp) cc_final: 0.6497 (ttm) REVERT: R 306 MET cc_start: 0.8248 (mmm) cc_final: 0.7876 (tpt) REVERT: R 376 MET cc_start: 0.8112 (mmm) cc_final: 0.7765 (tpp) outliers start: 26 outliers final: 26 residues processed: 156 average time/residue: 0.0854 time to fit residues: 19.7056 Evaluate side-chains 158 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 97 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 48 optimal weight: 0.0040 chunk 3 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 37 optimal weight: 0.0030 chunk 80 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 overall best weight: 0.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.190087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156980 restraints weight = 11092.046| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.06 r_work: 0.3696 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9708 Z= 0.090 Angle : 0.471 8.697 13193 Z= 0.249 Chirality : 0.041 0.253 1482 Planarity : 0.003 0.044 1698 Dihedral : 3.848 54.760 1351 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.41 % Allowed : 20.21 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.24), residues: 1226 helix: 1.06 (0.25), residues: 480 sheet: -1.87 (0.34), residues: 204 loop : -1.09 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.013 0.001 TYR N 60 PHE 0.024 0.001 PHE R 359 TRP 0.016 0.001 TRP B 82 HIS 0.001 0.000 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 9699) covalent geometry : angle 0.47094 (13177) SS BOND : bond 0.00075 ( 8) SS BOND : angle 0.55678 ( 16) hydrogen bonds : bond 0.02684 ( 357) hydrogen bonds : angle 4.10405 ( 1038) Misc. bond : bond 0.00000 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2824.26 seconds wall clock time: 48 minutes 58.00 seconds (2938.00 seconds total)