Starting phenix.real_space_refine on Wed Mar 4 13:24:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yw6_10959/03_2026/6yw6_10959.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yw6_10959/03_2026/6yw6_10959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6yw6_10959/03_2026/6yw6_10959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yw6_10959/03_2026/6yw6_10959.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6yw6_10959/03_2026/6yw6_10959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yw6_10959/03_2026/6yw6_10959.map" } resolution = 4.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 72 5.16 5 C 8815 2.51 5 N 2364 2.21 5 O 2566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 13823 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3177 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 26, 'TRANS': 369} Chain breaks: 2 Chain: "C" Number of atoms: 2645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2645 Classifications: {'peptide': 341} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 325} Chain breaks: 1 Chain: "D" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2291 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 11, 'TRANS': 158} Chain breaks: 1 Chain: "B" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2207 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 12, 'TRANS': 264} Chain breaks: 2 Chain: "G" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 703 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain breaks: 1 Chain: "F" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1357 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.06, per 1000 atoms: 0.22 Number of scatterers: 13823 At special positions: 0 Unit cell: (142.04, 104.94, 127.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 6 15.00 O 2566 8.00 N 2364 7.00 C 8815 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 610.9 milliseconds 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3238 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 21 sheets defined 37.8% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 63 through 69 Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.985A pdb=" N ARG A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.611A pdb=" N GLU A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 129 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 removed outlier: 3.526A pdb=" N LEU A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.878A pdb=" N THR A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.702A pdb=" N VAL A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.535A pdb=" N LYS A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.513A pdb=" N PHE A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.685A pdb=" N PHE A 287 " --> pdb=" O HIS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.955A pdb=" N VAL A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.796A pdb=" N THR A 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.511A pdb=" N ARG A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 354 removed outlier: 3.924A pdb=" N GLU A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.525A pdb=" N GLN A 373 " --> pdb=" O HIS A 370 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG A 374 " --> pdb=" O HIS A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 374' Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.509A pdb=" N PHE A 379 " --> pdb=" O TYR A 375 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 375 through 380' Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.541A pdb=" N CYS A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.700A pdb=" N TYR A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.346A pdb=" N CYS A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'D' and resid 13 through 24 removed outlier: 4.136A pdb=" N GLU D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 48 through 51 removed outlier: 3.943A pdb=" N ASP D 51 " --> pdb=" O PRO D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 72 through 80 removed outlier: 3.720A pdb=" N LEU D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG D 78 " --> pdb=" O GLU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 84 Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 117 through 134 removed outlier: 3.756A pdb=" N PHE D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 187 removed outlier: 4.336A pdb=" N VAL D 176 " --> pdb=" O ASP D 172 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE D 181 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 191 removed outlier: 4.273A pdb=" N ALA D 191 " --> pdb=" O GLY D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 188 through 191' Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'D' and resid 228 through 233 Processing helix chain 'D' and resid 236 through 245 removed outlier: 3.682A pdb=" N THR D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS D 245 " --> pdb=" O ILE D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 281 removed outlier: 3.638A pdb=" N HIS D 254 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 255 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 267 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 271 " --> pdb=" O ARG D 267 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 48 Processing helix chain 'E' and resid 63 through 82 removed outlier: 3.962A pdb=" N THR E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR E 70 " --> pdb=" O ARG E 66 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 99 Processing helix chain 'E' and resid 122 through 142 removed outlier: 4.269A pdb=" N ASP E 126 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY E 141 " --> pdb=" O ARG E 137 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU E 142 " --> pdb=" O GLN E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 149 Processing helix chain 'E' and resid 160 through 164 removed outlier: 3.931A pdb=" N PHE E 163 " --> pdb=" O TRP E 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.911A pdb=" N TRP B 89 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 186 through 201 removed outlier: 3.733A pdb=" N THR B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.674A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 3.925A pdb=" N ALA B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 235 " --> pdb=" O GLN B 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 230 through 235' Processing helix chain 'B' and resid 278 through 289 removed outlier: 3.568A pdb=" N LEU B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 removed outlier: 3.559A pdb=" N TYR B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 312 through 328 removed outlier: 4.242A pdb=" N GLU B 318 " --> pdb=" O PRO B 314 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 326 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.531A pdb=" N SER B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 352 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.845A pdb=" N GLY B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA B 359 " --> pdb=" O PHE B 355 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 86 removed outlier: 3.845A pdb=" N LEU G 80 " --> pdb=" O GLN G 76 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 90 removed outlier: 3.763A pdb=" N GLU G 90 " --> pdb=" O LYS G 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 87 through 90' Processing helix chain 'G' and resid 91 through 96 removed outlier: 3.578A pdb=" N GLN G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 114 removed outlier: 4.344A pdb=" N ASP G 104 " --> pdb=" O ARG G 100 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR G 111 " --> pdb=" O MET G 107 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS G 112 " --> pdb=" O LYS G 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY G 113 " --> pdb=" O TYR G 109 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE G 114 " --> pdb=" O ILE G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 137 removed outlier: 3.634A pdb=" N LYS G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA G 132 " --> pdb=" O TRP G 128 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA G 134 " --> pdb=" O GLU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 146 removed outlier: 3.508A pdb=" N LEU G 145 " --> pdb=" O ILE G 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 20 removed outlier: 3.812A pdb=" N LEU F 9 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN F 17 " --> pdb=" O ARG F 13 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA F 18 " --> pdb=" O ALA F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 41 removed outlier: 3.627A pdb=" N VAL F 40 " --> pdb=" O PRO F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 97 removed outlier: 3.569A pdb=" N LEU F 86 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE F 90 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET F 94 " --> pdb=" O PHE F 90 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET F 96 " --> pdb=" O ARG F 92 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 125 removed outlier: 3.601A pdb=" N THR F 123 " --> pdb=" O THR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 167 removed outlier: 3.972A pdb=" N VAL F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP F 133 " --> pdb=" O HIS F 129 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU F 141 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE F 142 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F 151 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG F 158 " --> pdb=" O ASN F 154 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU F 163 " --> pdb=" O ILE F 159 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE F 164 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.688A pdb=" N THR A 166 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE A 319 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 254 through 259 Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.801A pdb=" N GLY C 353 " --> pdb=" O GLY C 349 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY C 349 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLN C 344 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL C 334 " --> pdb=" O GLN C 344 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N CYS C 346 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE C 332 " --> pdb=" O CYS C 346 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR C 348 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 15 through 16 removed outlier: 3.658A pdb=" N ALA C 15 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 15 through 16 removed outlier: 3.658A pdb=" N ALA C 15 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C 32 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 55 through 61 removed outlier: 3.561A pdb=" N ARG C 66 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR C 77 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 82 " --> pdb=" O THR C 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 55 through 61 removed outlier: 3.561A pdb=" N ARG C 66 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR C 77 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA C 76 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 91 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 99 through 104 removed outlier: 6.882A pdb=" N GLY C 114 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL C 102 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA C 112 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TRP C 104 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LYS C 110 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS C 123 " --> pdb=" O PHE C 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.993A pdb=" N LEU C 157 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N SER C 170 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU C 194 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 205 through 210 removed outlier: 3.960A pdb=" N GLY C 207 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 247 through 252 removed outlier: 3.736A pdb=" N THR C 271 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER C 280 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 32 through 36 removed outlier: 3.582A pdb=" N PHE D 35 " --> pdb=" O TYR D 43 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 42 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 93 " --> pdb=" O ILE D 59 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 143 through 145 removed outlier: 3.790A pdb=" N THR D 151 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE D 223 " --> pdb=" O PHE D 165 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 19 through 20 removed outlier: 3.714A pdb=" N CYS B 20 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS B 30 " --> pdb=" O CYS B 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 180 through 181 removed outlier: 6.325A pdb=" N VAL B 155 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N SER B 304 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL B 157 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE B 301 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 242 through 243 Processing sheet with id=AC3, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.508A pdb=" N ILE F 118 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE F 114 " --> pdb=" O ILE F 74 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1155 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: 1.98 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4431 1.34 - 1.46: 3031 1.46 - 1.58: 6547 1.58 - 1.70: 11 1.70 - 1.82: 111 Bond restraints: 14131 Sorted by residual: bond pdb=" CA CYS C 342 " pdb=" C CYS C 342 " ideal model delta sigma weight residual 1.525 1.775 -0.250 2.10e-02 2.27e+03 1.41e+02 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 6.00e+01 bond pdb=" C4 ATP B 401 " pdb=" C5 ATP B 401 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.70e+01 bond pdb=" C5 ATP A 501 " pdb=" C6 ATP A 501 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.22e+01 bond pdb=" C5 ATP B 401 " pdb=" C6 ATP B 401 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.74e+01 ... (remaining 14126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 18918 3.90 - 7.79: 166 7.79 - 11.69: 18 11.69 - 15.59: 8 15.59 - 19.48: 5 Bond angle restraints: 19115 Sorted by residual: angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 120.39 19.48 1.00e+00 1.00e+00 3.80e+02 angle pdb=" PA ATP B 401 " pdb=" O3A ATP B 401 " pdb=" PB ATP B 401 " ideal model delta sigma weight residual 136.83 118.74 18.09 1.00e+00 1.00e+00 3.27e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 120.01 16.82 1.00e+00 1.00e+00 2.83e+02 angle pdb=" N LYS C 341 " pdb=" CA LYS C 341 " pdb=" C LYS C 341 " ideal model delta sigma weight residual 110.97 125.51 -14.54 1.09e+00 8.42e-01 1.78e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 127.47 12.40 1.00e+00 1.00e+00 1.54e+02 ... (remaining 19110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 8048 17.57 - 35.15: 406 35.15 - 52.72: 75 52.72 - 70.30: 7 70.30 - 87.87: 2 Dihedral angle restraints: 8538 sinusoidal: 3531 harmonic: 5007 Sorted by residual: dihedral pdb=" C LYS C 341 " pdb=" N LYS C 341 " pdb=" CA LYS C 341 " pdb=" CB LYS C 341 " ideal model delta harmonic sigma weight residual -122.60 -154.46 31.86 0 2.50e+00 1.60e-01 1.62e+02 dihedral pdb=" N LYS C 341 " pdb=" C LYS C 341 " pdb=" CA LYS C 341 " pdb=" CB LYS C 341 " ideal model delta harmonic sigma weight residual 122.80 153.65 -30.85 0 2.50e+00 1.60e-01 1.52e+02 dihedral pdb=" C CYS C 342 " pdb=" N CYS C 342 " pdb=" CA CYS C 342 " pdb=" CB CYS C 342 " ideal model delta harmonic sigma weight residual -122.60 -99.58 -23.02 0 2.50e+00 1.60e-01 8.48e+01 ... (remaining 8535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 2103 0.287 - 0.573: 1 0.573 - 0.860: 0 0.860 - 1.146: 0 1.146 - 1.433: 2 Chirality restraints: 2106 Sorted by residual: chirality pdb=" CA LYS C 341 " pdb=" N LYS C 341 " pdb=" C LYS C 341 " pdb=" CB LYS C 341 " both_signs ideal model delta sigma weight residual False 2.51 1.08 1.43 2.00e-01 2.50e+01 5.13e+01 chirality pdb=" CA CYS C 342 " pdb=" N CYS C 342 " pdb=" C CYS C 342 " pdb=" CB CYS C 342 " both_signs ideal model delta sigma weight residual False 2.51 3.79 -1.28 2.00e-01 2.50e+01 4.07e+01 chirality pdb=" CB ILE A 31 " pdb=" CA ILE A 31 " pdb=" CG1 ILE A 31 " pdb=" CG2 ILE A 31 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 2103 not shown) Planarity restraints: 2439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 139 " 0.048 5.00e-02 4.00e+02 7.33e-02 8.58e+00 pdb=" N PRO C 140 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 140 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 140 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 313 " -0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO B 314 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 314 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 314 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 266 " -0.023 2.00e-02 2.50e+03 2.13e-02 7.94e+00 pdb=" CG PHE B 266 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 266 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 266 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 266 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 266 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 266 " -0.000 2.00e-02 2.50e+03 ... (remaining 2436 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 817 2.71 - 3.26: 13138 3.26 - 3.81: 23021 3.81 - 4.35: 27496 4.35 - 4.90: 44734 Nonbonded interactions: 109206 Sorted by model distance: nonbonded pdb=" O GLY C 283 " pdb=" N LEU C 285 " model vdw 2.164 3.120 nonbonded pdb=" O LEU C 258 " pdb=" CD1 LEU C 269 " model vdw 2.203 3.460 nonbonded pdb=" OG SER C 343 " pdb=" OD1 ASP C 358 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR A 21 " pdb=" O LEU A 101 " model vdw 2.261 3.040 nonbonded pdb=" O ARG A 198 " pdb=" OG1 THR A 201 " model vdw 2.266 3.040 ... (remaining 109201 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.020 Find NCS groups from input model: 0.040 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 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 : 0.007 0.250 14131 Z= 0.378 Angle : 1.148 19.484 19115 Z= 0.702 Chirality : 0.071 1.433 2106 Planarity : 0.008 0.073 2439 Dihedral : 11.083 87.869 5300 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.20 % Favored : 93.51 % Rotamer: Outliers : 0.73 % Allowed : 4.71 % Favored : 94.56 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.53 (0.16), residues: 1694 helix: -4.03 (0.12), residues: 501 sheet: -2.61 (0.26), residues: 309 loop : -2.47 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 156 TYR 0.021 0.003 TYR D 146 PHE 0.048 0.003 PHE B 266 TRP 0.043 0.003 TRP C 16 HIS 0.017 0.003 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00704 (14131) covalent geometry : angle 1.14815 (19115) hydrogen bonds : bond 0.31109 ( 407) hydrogen bonds : angle 9.95677 ( 1155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 291 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8749 (m-30) cc_final: 0.7441 (p0) REVERT: A 90 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8538 (tm-30) REVERT: A 124 GLU cc_start: 0.8122 (pt0) cc_final: 0.7893 (pt0) REVERT: A 134 PHE cc_start: 0.9266 (m-80) cc_final: 0.8963 (m-80) REVERT: A 147 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9079 (pp) REVERT: A 199 ASP cc_start: 0.8088 (p0) cc_final: 0.7736 (m-30) REVERT: A 276 PHE cc_start: 0.8361 (p90) cc_final: 0.7867 (p90) REVERT: C 59 ASP cc_start: 0.7870 (t0) cc_final: 0.7467 (t0) REVERT: C 339 LYS cc_start: 0.9316 (mmtm) cc_final: 0.9115 (mmmt) REVERT: C 354 MET cc_start: 0.7165 (mpp) cc_final: 0.6849 (mpp) REVERT: D 5 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7507 (mm-30) REVERT: D 115 MET cc_start: 0.8747 (mmp) cc_final: 0.8419 (mmm) REVERT: E 70 TYR cc_start: 0.8022 (t80) cc_final: 0.7792 (t80) REVERT: E 116 ILE cc_start: 0.8650 (mt) cc_final: 0.8449 (mm) REVERT: E 150 ASP cc_start: 0.8299 (t70) cc_final: 0.7618 (t0) REVERT: E 166 ARG cc_start: 0.9220 (mmt-90) cc_final: 0.7964 (tpt170) REVERT: B 147 TYR cc_start: 0.8952 (t80) cc_final: 0.8546 (t80) REVERT: B 158 ASP cc_start: 0.8756 (t0) cc_final: 0.8550 (t0) REVERT: B 231 GLN cc_start: 0.8531 (mt0) cc_final: 0.8271 (mp10) REVERT: B 281 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8345 (tm) REVERT: G 148 ARG cc_start: 0.5359 (mmm160) cc_final: 0.3171 (ptt180) REVERT: F 125 GLN cc_start: 0.8304 (mp10) cc_final: 0.7948 (mp10) outliers start: 11 outliers final: 2 residues processed: 299 average time/residue: 0.1315 time to fit residues: 54.8996 Evaluate side-chains 164 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 160 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 205 GLN C 222 HIS ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS E 135 GLN B 30 HIS ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.090513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.070504 restraints weight = 60995.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.072048 restraints weight = 40274.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.072763 restraints weight = 30472.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.073475 restraints weight = 24189.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.073617 restraints weight = 21810.824| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14131 Z= 0.212 Angle : 0.717 9.882 19115 Z= 0.380 Chirality : 0.048 0.200 2106 Planarity : 0.006 0.104 2439 Dihedral : 7.911 80.723 1930 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.40 (0.18), residues: 1694 helix: -2.61 (0.17), residues: 555 sheet: -2.09 (0.28), residues: 289 loop : -1.98 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 294 TYR 0.017 0.002 TYR D 146 PHE 0.022 0.002 PHE B 266 TRP 0.026 0.002 TRP C 60 HIS 0.007 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00463 (14131) covalent geometry : angle 0.71727 (19115) hydrogen bonds : bond 0.05600 ( 407) hydrogen bonds : angle 6.44236 ( 1155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8083 (tm-30) REVERT: A 199 ASP cc_start: 0.8101 (p0) cc_final: 0.7580 (m-30) REVERT: A 276 PHE cc_start: 0.8030 (p90) cc_final: 0.7677 (p90) REVERT: A 348 LYS cc_start: 0.9514 (tttp) cc_final: 0.9251 (tptt) REVERT: A 408 CYS cc_start: 0.8455 (p) cc_final: 0.8130 (t) REVERT: C 54 GLN cc_start: 0.7316 (mt0) cc_final: 0.6842 (tm-30) REVERT: C 354 MET cc_start: 0.7686 (mpp) cc_final: 0.7154 (mpp) REVERT: D 183 GLN cc_start: 0.9158 (tp40) cc_final: 0.8767 (tp-100) REVERT: E 150 ASP cc_start: 0.7679 (t70) cc_final: 0.7314 (t0) REVERT: E 166 ARG cc_start: 0.9198 (mmt-90) cc_final: 0.8207 (tpt170) REVERT: B 353 MET cc_start: 0.7172 (mmp) cc_final: 0.6865 (mmm) REVERT: G 148 ARG cc_start: 0.5253 (mmm160) cc_final: 0.3128 (ptt180) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1059 time to fit residues: 33.9026 Evaluate side-chains 151 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN D 21 ASN D 263 HIS E 90 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.090287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.068964 restraints weight = 61140.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.070625 restraints weight = 40285.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.071814 restraints weight = 30228.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.072869 restraints weight = 24948.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.073197 restraints weight = 21633.984| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14131 Z= 0.190 Angle : 0.671 11.671 19115 Z= 0.352 Chirality : 0.047 0.200 2106 Planarity : 0.005 0.068 2439 Dihedral : 7.328 75.056 1930 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % 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: -2.75 (0.19), residues: 1694 helix: -1.80 (0.19), residues: 573 sheet: -1.78 (0.28), residues: 298 loop : -1.76 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 284 TYR 0.016 0.002 TYR D 146 PHE 0.024 0.002 PHE D 63 TRP 0.019 0.002 TRP C 60 HIS 0.005 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00416 (14131) covalent geometry : angle 0.67111 (19115) hydrogen bonds : bond 0.04639 ( 407) hydrogen bonds : angle 5.89806 ( 1155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8255 (tm-30) REVERT: A 147 LEU cc_start: 0.9311 (pp) cc_final: 0.9108 (pp) REVERT: A 199 ASP cc_start: 0.8170 (p0) cc_final: 0.7785 (m-30) REVERT: A 243 ASN cc_start: 0.9107 (t0) cc_final: 0.8740 (p0) REVERT: A 276 PHE cc_start: 0.7909 (p90) cc_final: 0.7592 (p90) REVERT: A 374 ARG cc_start: 0.8115 (ptp90) cc_final: 0.7756 (ttp80) REVERT: C 54 GLN cc_start: 0.7518 (mt0) cc_final: 0.6945 (tm-30) REVERT: C 235 MET cc_start: 0.8023 (mmp) cc_final: 0.7044 (mmp) REVERT: D 183 GLN cc_start: 0.9168 (tp40) cc_final: 0.8819 (tp-100) REVERT: D 266 MET cc_start: 0.7846 (ttm) cc_final: 0.7631 (ttm) REVERT: E 166 ARG cc_start: 0.9227 (mmt-90) cc_final: 0.8269 (tpt170) REVERT: B 323 GLN cc_start: 0.9343 (tt0) cc_final: 0.9039 (tm-30) REVERT: B 353 MET cc_start: 0.7232 (mmp) cc_final: 0.6922 (mmm) REVERT: G 148 ARG cc_start: 0.5269 (mmm160) cc_final: 0.3230 (ptp90) REVERT: F 96 MET cc_start: 0.6721 (ttp) cc_final: 0.5321 (ttm) REVERT: F 143 ASP cc_start: 0.8513 (p0) cc_final: 0.8257 (p0) outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.1001 time to fit residues: 29.7546 Evaluate side-chains 149 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 67 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 153 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 192 HIS ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.091727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.070519 restraints weight = 58775.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.072395 restraints weight = 38610.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.073841 restraints weight = 28933.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.074807 restraints weight = 23493.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.075501 restraints weight = 20302.915| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14131 Z= 0.128 Angle : 0.622 11.425 19115 Z= 0.323 Chirality : 0.046 0.196 2106 Planarity : 0.005 0.065 2439 Dihedral : 6.957 80.884 1930 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.07 % Allowed : 2.92 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % 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: -2.27 (0.20), residues: 1694 helix: -1.26 (0.20), residues: 564 sheet: -1.55 (0.28), residues: 312 loop : -1.56 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 284 TYR 0.016 0.001 TYR D 146 PHE 0.021 0.002 PHE C 266 TRP 0.017 0.001 TRP C 60 HIS 0.008 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00287 (14131) covalent geometry : angle 0.62179 (19115) hydrogen bonds : bond 0.03959 ( 407) hydrogen bonds : angle 5.55107 ( 1155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8820 (mppt) cc_final: 0.8422 (mttm) REVERT: A 243 ASN cc_start: 0.9036 (t0) cc_final: 0.8648 (p0) REVERT: A 276 PHE cc_start: 0.7380 (p90) cc_final: 0.7091 (p90) REVERT: A 408 CYS cc_start: 0.8420 (p) cc_final: 0.7781 (t) REVERT: C 189 MET cc_start: 0.7218 (mtm) cc_final: 0.6713 (mmt) REVERT: E 86 ASN cc_start: 0.8467 (p0) cc_final: 0.8226 (t0) REVERT: E 166 ARG cc_start: 0.9162 (mmt-90) cc_final: 0.8223 (tpt170) REVERT: B 323 GLN cc_start: 0.9325 (tt0) cc_final: 0.9041 (tm-30) REVERT: B 353 MET cc_start: 0.7320 (mmp) cc_final: 0.6840 (mmm) REVERT: G 148 ARG cc_start: 0.5339 (mmm160) cc_final: 0.3201 (ptt180) REVERT: F 23 GLU cc_start: 0.8505 (pt0) cc_final: 0.8193 (pt0) REVERT: F 96 MET cc_start: 0.6608 (ttp) cc_final: 0.5081 (ttp) REVERT: F 149 MET cc_start: 0.8950 (mmt) cc_final: 0.8740 (mmm) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.1138 time to fit residues: 34.2794 Evaluate side-chains 140 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 150 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN E 90 GLN B 30 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.089632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.068629 restraints weight = 60618.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.070525 restraints weight = 40686.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.071876 restraints weight = 30797.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.072682 restraints weight = 25229.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.073427 restraints weight = 22051.871| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14131 Z= 0.201 Angle : 0.672 13.808 19115 Z= 0.348 Chirality : 0.047 0.196 2106 Planarity : 0.005 0.068 2439 Dihedral : 6.919 80.603 1930 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % 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: -2.16 (0.20), residues: 1694 helix: -1.19 (0.20), residues: 573 sheet: -1.47 (0.29), residues: 312 loop : -1.49 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 230 TYR 0.012 0.001 TYR D 146 PHE 0.019 0.002 PHE D 63 TRP 0.014 0.002 TRP C 60 HIS 0.006 0.001 HIS D 70 Details of bonding type rmsd covalent geometry : bond 0.00445 (14131) covalent geometry : angle 0.67228 (19115) hydrogen bonds : bond 0.04018 ( 407) hydrogen bonds : angle 5.58277 ( 1155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8788 (mppt) cc_final: 0.8162 (mtmm) REVERT: A 124 GLU cc_start: 0.7983 (pt0) cc_final: 0.7745 (pt0) REVERT: A 199 ASP cc_start: 0.8396 (m-30) cc_final: 0.8190 (m-30) REVERT: A 243 ASN cc_start: 0.9075 (t0) cc_final: 0.8698 (p0) REVERT: A 276 PHE cc_start: 0.7626 (p90) cc_final: 0.7278 (p90) REVERT: A 408 CYS cc_start: 0.8530 (p) cc_final: 0.8017 (t) REVERT: C 235 MET cc_start: 0.7807 (mmp) cc_final: 0.6659 (mmp) REVERT: C 354 MET cc_start: 0.8057 (pmm) cc_final: 0.7701 (pmm) REVERT: E 70 TYR cc_start: 0.7876 (t80) cc_final: 0.7578 (t80) REVERT: E 166 ARG cc_start: 0.9132 (mmt-90) cc_final: 0.8279 (tpt170) REVERT: B 147 TYR cc_start: 0.8778 (t80) cc_final: 0.8339 (t80) REVERT: B 323 GLN cc_start: 0.9305 (tt0) cc_final: 0.9015 (tm-30) REVERT: B 353 MET cc_start: 0.7371 (mmp) cc_final: 0.6850 (mmm) REVERT: G 148 ARG cc_start: 0.5496 (mmm160) cc_final: 0.3293 (ptt180) REVERT: F 96 MET cc_start: 0.6769 (ttp) cc_final: 0.4974 (ttt) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.0941 time to fit residues: 26.6491 Evaluate side-chains 144 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 27 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 81 optimal weight: 0.0470 chunk 160 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 102 optimal weight: 0.0050 chunk 42 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 overall best weight: 4.0098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN E 90 GLN B 30 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.088367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.067596 restraints weight = 60581.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.069233 restraints weight = 39988.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.070544 restraints weight = 30080.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.071493 restraints weight = 24655.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.071935 restraints weight = 21330.033| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 14131 Z= 0.245 Angle : 0.720 12.154 19115 Z= 0.370 Chirality : 0.048 0.198 2106 Planarity : 0.005 0.065 2439 Dihedral : 7.038 84.493 1930 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.07 % Allowed : 3.32 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.18 (0.20), residues: 1694 helix: -1.12 (0.20), residues: 570 sheet: -1.47 (0.29), residues: 304 loop : -1.58 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 97 TYR 0.016 0.002 TYR B 170 PHE 0.034 0.002 PHE D 63 TRP 0.016 0.002 TRP C 357 HIS 0.012 0.002 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00540 (14131) covalent geometry : angle 0.71961 (19115) hydrogen bonds : bond 0.04072 ( 407) hydrogen bonds : angle 5.71224 ( 1155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8804 (mppt) cc_final: 0.8505 (mttt) REVERT: A 124 GLU cc_start: 0.8027 (pt0) cc_final: 0.7780 (pt0) REVERT: A 408 CYS cc_start: 0.8587 (p) cc_final: 0.8121 (t) REVERT: C 354 MET cc_start: 0.8153 (pmm) cc_final: 0.7615 (pmm) REVERT: E 70 TYR cc_start: 0.7760 (t80) cc_final: 0.7325 (t80) REVERT: E 86 ASN cc_start: 0.8717 (p0) cc_final: 0.8238 (m-40) REVERT: E 90 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8285 (pp30) REVERT: E 166 ARG cc_start: 0.9100 (mmt-90) cc_final: 0.8329 (tpt170) REVERT: B 323 GLN cc_start: 0.9278 (tt0) cc_final: 0.8964 (tm-30) REVERT: B 353 MET cc_start: 0.7350 (mmp) cc_final: 0.6925 (mmm) REVERT: G 148 ARG cc_start: 0.5461 (mmm160) cc_final: 0.3140 (ptt180) REVERT: F 96 MET cc_start: 0.6763 (ttp) cc_final: 0.5263 (ttt) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.0925 time to fit residues: 25.2824 Evaluate side-chains 138 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.089541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.068256 restraints weight = 59732.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.070155 restraints weight = 39396.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.071560 restraints weight = 29504.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.072543 restraints weight = 24060.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.073240 restraints weight = 20792.104| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14131 Z= 0.174 Angle : 0.667 12.361 19115 Z= 0.345 Chirality : 0.047 0.202 2106 Planarity : 0.004 0.062 2439 Dihedral : 6.823 82.928 1930 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.07 % Allowed : 1.73 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % 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: -2.03 (0.20), residues: 1694 helix: -0.96 (0.21), residues: 566 sheet: -1.59 (0.29), residues: 295 loop : -1.43 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 97 TYR 0.019 0.002 TYR D 146 PHE 0.030 0.002 PHE D 63 TRP 0.015 0.001 TRP C 60 HIS 0.009 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00393 (14131) covalent geometry : angle 0.66736 (19115) hydrogen bonds : bond 0.03828 ( 407) hydrogen bonds : angle 5.56808 ( 1155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8837 (mppt) cc_final: 0.8456 (mtmt) REVERT: A 90 GLU cc_start: 0.9166 (tt0) cc_final: 0.8874 (tt0) REVERT: A 124 GLU cc_start: 0.8024 (pt0) cc_final: 0.7793 (pt0) REVERT: A 408 CYS cc_start: 0.8537 (p) cc_final: 0.8005 (t) REVERT: C 189 MET cc_start: 0.7769 (ptp) cc_final: 0.7301 (ptt) REVERT: C 235 MET cc_start: 0.8280 (mmp) cc_final: 0.6441 (mmp) REVERT: C 354 MET cc_start: 0.8147 (pmm) cc_final: 0.7709 (pmm) REVERT: E 70 TYR cc_start: 0.7709 (t80) cc_final: 0.7222 (t80) REVERT: E 86 ASN cc_start: 0.8734 (p0) cc_final: 0.8129 (m-40) REVERT: E 166 ARG cc_start: 0.9069 (mmt-90) cc_final: 0.8367 (tpt170) REVERT: B 147 TYR cc_start: 0.8683 (t80) cc_final: 0.8277 (t80) REVERT: B 323 GLN cc_start: 0.9269 (tt0) cc_final: 0.8974 (tm-30) REVERT: B 353 MET cc_start: 0.7393 (mmp) cc_final: 0.6888 (mmm) REVERT: G 148 ARG cc_start: 0.5399 (mmm160) cc_final: 0.3052 (ptt180) REVERT: F 96 MET cc_start: 0.6627 (ttp) cc_final: 0.5189 (ttt) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.0976 time to fit residues: 27.6873 Evaluate side-chains 138 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 82 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.091107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.069881 restraints weight = 58481.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.071669 restraints weight = 38410.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.073086 restraints weight = 28921.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.073799 restraints weight = 23513.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.074713 restraints weight = 20736.489| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14131 Z= 0.126 Angle : 0.643 11.633 19115 Z= 0.328 Chirality : 0.046 0.195 2106 Planarity : 0.004 0.061 2439 Dihedral : 6.568 80.561 1930 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.07 % Allowed : 1.33 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % 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: -1.84 (0.20), residues: 1694 helix: -0.74 (0.21), residues: 569 sheet: -1.63 (0.29), residues: 301 loop : -1.30 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 267 TYR 0.020 0.001 TYR D 146 PHE 0.024 0.002 PHE D 63 TRP 0.036 0.002 TRP C 219 HIS 0.009 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00285 (14131) covalent geometry : angle 0.64349 (19115) hydrogen bonds : bond 0.03535 ( 407) hydrogen bonds : angle 5.34520 ( 1155) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8804 (mppt) cc_final: 0.8270 (mtmt) REVERT: A 124 GLU cc_start: 0.8089 (pt0) cc_final: 0.7737 (pt0) REVERT: A 408 CYS cc_start: 0.8535 (p) cc_final: 0.8026 (t) REVERT: C 189 MET cc_start: 0.7839 (ptp) cc_final: 0.7316 (ptt) REVERT: C 235 MET cc_start: 0.8284 (mmp) cc_final: 0.6405 (mmp) REVERT: C 354 MET cc_start: 0.8087 (pmm) cc_final: 0.7763 (pmm) REVERT: E 70 TYR cc_start: 0.7783 (t80) cc_final: 0.7299 (t80) REVERT: E 86 ASN cc_start: 0.8787 (p0) cc_final: 0.8202 (m-40) REVERT: E 90 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8065 (pp30) REVERT: E 166 ARG cc_start: 0.9024 (mmt-90) cc_final: 0.8320 (tpt170) REVERT: B 147 TYR cc_start: 0.8606 (t80) cc_final: 0.8160 (t80) REVERT: B 323 GLN cc_start: 0.9219 (tt0) cc_final: 0.8925 (tm-30) REVERT: B 353 MET cc_start: 0.7308 (mmp) cc_final: 0.6824 (mmm) REVERT: G 148 ARG cc_start: 0.5297 (mmm160) cc_final: 0.3021 (ptt180) REVERT: F 96 MET cc_start: 0.6536 (ttp) cc_final: 0.5027 (ttt) REVERT: F 148 GLU cc_start: 0.8968 (mp0) cc_final: 0.8626 (mp0) REVERT: F 159 ILE cc_start: 0.9261 (mm) cc_final: 0.8833 (tp) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.0927 time to fit residues: 27.3725 Evaluate side-chains 142 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 154 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.0000 chunk 98 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN E 90 GLN B 30 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.088660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.067512 restraints weight = 60965.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.069291 restraints weight = 40424.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.070740 restraints weight = 30333.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.071678 restraints weight = 24710.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.072255 restraints weight = 21426.603| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14131 Z= 0.224 Angle : 0.711 11.535 19115 Z= 0.367 Chirality : 0.048 0.192 2106 Planarity : 0.005 0.064 2439 Dihedral : 6.922 87.179 1930 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.07 % Allowed : 0.86 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.89 (0.20), residues: 1694 helix: -0.78 (0.21), residues: 564 sheet: -1.53 (0.29), residues: 285 loop : -1.41 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 230 TYR 0.024 0.002 TYR A 125 PHE 0.033 0.002 PHE D 63 TRP 0.022 0.002 TRP C 219 HIS 0.009 0.002 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00500 (14131) covalent geometry : angle 0.71088 (19115) hydrogen bonds : bond 0.03960 ( 407) hydrogen bonds : angle 5.61533 ( 1155) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8859 (mppt) cc_final: 0.8549 (mtmt) REVERT: A 90 GLU cc_start: 0.9184 (tt0) cc_final: 0.8961 (tt0) REVERT: A 124 GLU cc_start: 0.7985 (pt0) cc_final: 0.7752 (pt0) REVERT: A 408 CYS cc_start: 0.8524 (p) cc_final: 0.8037 (t) REVERT: C 189 MET cc_start: 0.7905 (ptp) cc_final: 0.7420 (ptt) REVERT: C 354 MET cc_start: 0.8037 (pmm) cc_final: 0.7614 (pmm) REVERT: E 19 MET cc_start: 0.9009 (pmm) cc_final: 0.8780 (pmm) REVERT: E 70 TYR cc_start: 0.7849 (t80) cc_final: 0.7295 (t80) REVERT: E 86 ASN cc_start: 0.8771 (p0) cc_final: 0.8229 (m-40) REVERT: E 90 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8090 (pp30) REVERT: E 166 ARG cc_start: 0.9031 (mmt-90) cc_final: 0.8380 (tpt170) REVERT: B 323 GLN cc_start: 0.9272 (tt0) cc_final: 0.8958 (tm-30) REVERT: B 353 MET cc_start: 0.7378 (mmp) cc_final: 0.6876 (mmm) REVERT: G 148 ARG cc_start: 0.5397 (mmm160) cc_final: 0.3149 (ptt-90) REVERT: F 96 MET cc_start: 0.6499 (ttp) cc_final: 0.5126 (ttt) REVERT: F 148 GLU cc_start: 0.8943 (mp0) cc_final: 0.8581 (mp0) REVERT: F 159 ILE cc_start: 0.9257 (mm) cc_final: 0.8805 (tp) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.0905 time to fit residues: 25.5787 Evaluate side-chains 136 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 0.0770 chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 118 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 129 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN D 21 ASN D 263 HIS E 90 GLN B 165 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.092544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.072006 restraints weight = 58585.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.073785 restraints weight = 37775.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.075063 restraints weight = 27940.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.076064 restraints weight = 22766.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.076559 restraints weight = 19650.039| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14131 Z= 0.110 Angle : 0.635 10.713 19115 Z= 0.322 Chirality : 0.046 0.198 2106 Planarity : 0.004 0.060 2439 Dihedral : 6.412 87.299 1930 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.13 % Allowed : 0.13 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % 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: -1.58 (0.20), residues: 1694 helix: -0.49 (0.22), residues: 564 sheet: -1.51 (0.29), residues: 307 loop : -1.15 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 230 TYR 0.022 0.001 TYR A 125 PHE 0.023 0.001 PHE A 287 TRP 0.027 0.001 TRP C 219 HIS 0.009 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00250 (14131) covalent geometry : angle 0.63539 (19115) hydrogen bonds : bond 0.03429 ( 407) hydrogen bonds : angle 5.17094 ( 1155) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8777 (mppt) cc_final: 0.8352 (mtmt) REVERT: A 34 CYS cc_start: 0.7670 (p) cc_final: 0.7275 (m) REVERT: A 90 GLU cc_start: 0.9191 (tt0) cc_final: 0.8942 (tt0) REVERT: C 189 MET cc_start: 0.7702 (ptp) cc_final: 0.7209 (ptt) REVERT: D 275 LYS cc_start: 0.9293 (tmmt) cc_final: 0.8975 (ttmt) REVERT: E 70 TYR cc_start: 0.7815 (t80) cc_final: 0.7570 (t80) REVERT: E 86 ASN cc_start: 0.8729 (p0) cc_final: 0.8173 (m110) REVERT: E 166 ARG cc_start: 0.8918 (mmt-90) cc_final: 0.8285 (tpt170) REVERT: B 147 TYR cc_start: 0.8421 (t80) cc_final: 0.8010 (t80) REVERT: B 323 GLN cc_start: 0.9196 (tt0) cc_final: 0.8919 (tm-30) REVERT: B 353 MET cc_start: 0.7307 (mmp) cc_final: 0.6865 (mmm) REVERT: G 148 ARG cc_start: 0.5277 (mmm160) cc_final: 0.3171 (ptt180) REVERT: F 96 MET cc_start: 0.6347 (ttp) cc_final: 0.4846 (ttt) REVERT: F 148 GLU cc_start: 0.8957 (mp0) cc_final: 0.8604 (mp0) REVERT: F 159 ILE cc_start: 0.9274 (mm) cc_final: 0.8854 (tp) outliers start: 2 outliers final: 0 residues processed: 193 average time/residue: 0.0886 time to fit residues: 27.5824 Evaluate side-chains 149 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 141 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 263 HIS E 90 GLN B 30 HIS B 165 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.088787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.068023 restraints weight = 60945.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.069649 restraints weight = 41160.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.070931 restraints weight = 31226.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071846 restraints weight = 25770.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.072470 restraints weight = 22482.915| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 14131 Z= 0.229 Angle : 0.704 11.794 19115 Z= 0.363 Chirality : 0.048 0.248 2106 Planarity : 0.005 0.064 2439 Dihedral : 6.688 79.467 1930 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.13 % Allowed : 0.27 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % 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: -1.76 (0.20), residues: 1694 helix: -0.67 (0.21), residues: 564 sheet: -1.56 (0.29), residues: 281 loop : -1.29 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 230 TYR 0.014 0.002 TYR A 375 PHE 0.032 0.002 PHE D 63 TRP 0.017 0.002 TRP C 219 HIS 0.007 0.002 HIS D 70 Details of bonding type rmsd covalent geometry : bond 0.00512 (14131) covalent geometry : angle 0.70399 (19115) hydrogen bonds : bond 0.03893 ( 407) hydrogen bonds : angle 5.54751 ( 1155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2210.50 seconds wall clock time: 39 minutes 9.41 seconds (2349.41 seconds total)