Starting phenix.real_space_refine on Thu Jul 31 23:09:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yw6_10959/07_2025/6yw6_10959.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yw6_10959/07_2025/6yw6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6yw6_10959/07_2025/6yw6_10959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yw6_10959/07_2025/6yw6_10959.map" model { file = "/net/cci-nas-00/data/ceres_data/6yw6_10959/07_2025/6yw6_10959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yw6_10959/07_2025/6yw6_10959.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.33, per 1000 atoms: 0.60 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: 3.19 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.78 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: 3.75 Time building geometry restraints manager: 3.81 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: 1.160 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.260 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.350 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.043 0.003 TRP C 16 HIS 0.017 0.003 HIS C 151 PHE 0.048 0.003 PHE B 266 TYR 0.021 0.003 TYR D 146 ARG 0.013 0.001 ARG F 156 Details of bonding type rmsd hydrogen bonds : bond 0.31109 ( 407) hydrogen bonds : angle 9.95677 ( 1155) covalent geometry : bond 0.00704 (14131) covalent geometry : angle 1.14815 (19115) *********************** 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 : 1.660 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: 0.3193 time to fit residues: 132.9757 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 : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.1980 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 43 optimal weight: 0.0970 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 176 HIS A 205 GLN C 222 HIS C 256 ASN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS D 278 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.093560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071605 restraints weight = 58746.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.073583 restraints weight = 38789.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.074997 restraints weight = 29050.990| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2724 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= 0.135 Angle : 0.663 10.093 19115 Z= 0.351 Chirality : 0.046 0.212 2106 Planarity : 0.006 0.115 2439 Dihedral : 7.718 87.142 1930 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.18), residues: 1694 helix: -2.58 (0.17), residues: 546 sheet: -2.09 (0.27), residues: 297 loop : -1.94 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 60 HIS 0.005 0.001 HIS B 30 PHE 0.017 0.002 PHE C 6 TYR 0.018 0.001 TYR D 146 ARG 0.011 0.001 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.05176 ( 407) hydrogen bonds : angle 6.24045 ( 1155) covalent geometry : bond 0.00294 (14131) covalent geometry : angle 0.66303 (19115) *********************** 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 235 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.696 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: A 18 LYS cc_start: 0.8440 (mppt) cc_final: 0.8215 (mttm) REVERT: A 118 ASN cc_start: 0.7820 (m110) cc_final: 0.7614 (t0) REVERT: A 124 GLU cc_start: 0.7895 (pt0) cc_final: 0.7617 (pt0) REVERT: A 243 ASN cc_start: 0.9117 (t0) cc_final: 0.8791 (p0) REVERT: A 276 PHE cc_start: 0.8079 (p90) cc_final: 0.7714 (p90) REVERT: A 348 LYS cc_start: 0.9472 (tttp) cc_final: 0.9060 (tptp) REVERT: A 408 CYS cc_start: 0.8543 (p) cc_final: 0.8076 (t) REVERT: C 54 GLN cc_start: 0.7101 (mt0) cc_final: 0.6610 (tm-30) REVERT: C 189 MET cc_start: 0.6846 (mtm) cc_final: 0.6627 (mmt) REVERT: D 183 GLN cc_start: 0.9219 (tp40) cc_final: 0.8781 (tp-100) REVERT: D 207 LEU cc_start: 0.8844 (mt) cc_final: 0.8618 (pt) REVERT: E 150 ASP cc_start: 0.7723 (t70) cc_final: 0.7375 (t0) REVERT: E 166 ARG cc_start: 0.9206 (mmt-90) cc_final: 0.8071 (tpp-160) REVERT: B 147 TYR cc_start: 0.8765 (t80) cc_final: 0.8546 (t80) REVERT: B 158 ASP cc_start: 0.8520 (t0) cc_final: 0.8279 (t0) REVERT: B 353 MET cc_start: 0.7070 (mmp) cc_final: 0.6729 (mmm) REVERT: G 148 ARG cc_start: 0.5090 (mmm160) cc_final: 0.3184 (ptp90) REVERT: F 96 MET cc_start: 0.6335 (ttp) cc_final: 0.4998 (ttm) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2462 time to fit residues: 85.5440 Evaluate side-chains 168 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS D 278 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS ** F 28 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 = 0.3923 r_free = 0.3923 target = 0.092615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.070693 restraints weight = 60235.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.072768 restraints weight = 37572.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.074376 restraints weight = 27235.757| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3211 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= 0.154 Angle : 0.640 11.875 19115 Z= 0.334 Chirality : 0.046 0.203 2106 Planarity : 0.005 0.067 2439 Dihedral : 7.109 74.554 1930 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.19), residues: 1694 helix: -1.84 (0.19), residues: 563 sheet: -1.77 (0.27), residues: 316 loop : -1.70 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 60 HIS 0.008 0.001 HIS B 30 PHE 0.016 0.002 PHE B 266 TYR 0.013 0.001 TYR D 146 ARG 0.009 0.001 ARG C 284 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 407) hydrogen bonds : angle 5.72649 ( 1155) covalent geometry : bond 0.00338 (14131) covalent geometry : angle 0.63990 (19115) *********************** 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 200 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.657 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: A 18 LYS cc_start: 0.8567 (mppt) cc_final: 0.8309 (mtmm) REVERT: A 118 ASN cc_start: 0.8003 (m110) cc_final: 0.7779 (t0) REVERT: A 243 ASN cc_start: 0.9182 (t0) cc_final: 0.8780 (p0) REVERT: A 276 PHE cc_start: 0.8050 (p90) cc_final: 0.7629 (p90) REVERT: A 348 LYS cc_start: 0.9442 (tttp) cc_final: 0.8991 (tptm) REVERT: C 54 GLN cc_start: 0.7442 (mt0) cc_final: 0.6735 (tm-30) REVERT: C 189 MET cc_start: 0.7166 (mtm) cc_final: 0.6712 (mmt) REVERT: C 235 MET cc_start: 0.8016 (mmp) cc_final: 0.7023 (mmp) REVERT: D 5 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7876 (mm-30) REVERT: D 183 GLN cc_start: 0.9245 (tp40) cc_final: 0.8812 (tp-100) REVERT: D 266 MET cc_start: 0.7996 (ttm) cc_final: 0.7737 (ttm) REVERT: E 86 ASN cc_start: 0.9297 (t0) cc_final: 0.8838 (p0) REVERT: E 125 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8693 (mm-30) REVERT: E 166 ARG cc_start: 0.9175 (mmt-90) cc_final: 0.8146 (tpt170) REVERT: B 147 TYR cc_start: 0.8786 (t80) cc_final: 0.8538 (t80) REVERT: B 158 ASP cc_start: 0.8650 (t0) cc_final: 0.8439 (t0) REVERT: B 309 MET cc_start: 0.8569 (tmm) cc_final: 0.8328 (tmm) REVERT: B 323 GLN cc_start: 0.9339 (tt0) cc_final: 0.9008 (tm-30) REVERT: B 353 MET cc_start: 0.7030 (mmp) cc_final: 0.6733 (mmm) REVERT: G 148 ARG cc_start: 0.5039 (mmm160) cc_final: 0.3182 (ptt180) REVERT: F 143 ASP cc_start: 0.8565 (p0) cc_final: 0.8303 (p0) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2398 time to fit residues: 72.2509 Evaluate side-chains 156 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 120 optimal weight: 0.0980 chunk 25 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 0.0870 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 0.0070 chunk 68 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 81 optimal weight: 0.2980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 192 HIS A 395 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN F 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.095072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.072919 restraints weight = 58176.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.075204 restraints weight = 36057.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.076882 restraints weight = 25888.131| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14131 Z= 0.109 Angle : 0.596 12.061 19115 Z= 0.308 Chirality : 0.046 0.206 2106 Planarity : 0.005 0.063 2439 Dihedral : 6.816 88.695 1930 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.19), residues: 1694 helix: -1.39 (0.20), residues: 569 sheet: -1.52 (0.28), residues: 313 loop : -1.56 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 60 HIS 0.007 0.001 HIS B 30 PHE 0.022 0.002 PHE C 266 TYR 0.015 0.001 TYR A 125 ARG 0.017 0.001 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 407) hydrogen bonds : angle 5.32757 ( 1155) covalent geometry : bond 0.00239 (14131) covalent geometry : angle 0.59581 (19115) *********************** 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 209 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 1.528 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: 0.8777 (mppt) cc_final: 0.8196 (mtmm) REVERT: A 118 ASN cc_start: 0.8042 (m110) cc_final: 0.7765 (t0) REVERT: A 147 LEU cc_start: 0.9228 (pp) cc_final: 0.9026 (pp) REVERT: A 243 ASN cc_start: 0.9150 (t0) cc_final: 0.8747 (p0) REVERT: A 276 PHE cc_start: 0.7540 (p90) cc_final: 0.7179 (p90) REVERT: A 408 CYS cc_start: 0.8745 (p) cc_final: 0.8069 (t) REVERT: C 235 MET cc_start: 0.7963 (mmp) cc_final: 0.6859 (mmp) REVERT: C 354 MET cc_start: 0.7420 (pmm) cc_final: 0.7124 (pmm) REVERT: D 5 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7849 (mm-30) REVERT: D 183 GLN cc_start: 0.9230 (tp40) cc_final: 0.8987 (tp-100) REVERT: E 86 ASN cc_start: 0.9273 (t0) cc_final: 0.8793 (p0) REVERT: E 125 GLU cc_start: 0.9335 (mt-10) cc_final: 0.8797 (mm-30) REVERT: E 166 ARG cc_start: 0.9121 (mmt-90) cc_final: 0.8087 (tpt170) REVERT: E 167 GLN cc_start: 0.8103 (pm20) cc_final: 0.7791 (pm20) REVERT: B 147 TYR cc_start: 0.8630 (t80) cc_final: 0.8306 (t80) REVERT: B 228 GLU cc_start: 0.8245 (mp0) cc_final: 0.7966 (pp20) REVERT: B 323 GLN cc_start: 0.9326 (tt0) cc_final: 0.9061 (tm-30) REVERT: B 353 MET cc_start: 0.7187 (mmp) cc_final: 0.6666 (mmm) REVERT: G 148 ARG cc_start: 0.5209 (mmm160) cc_final: 0.3356 (ptt180) outliers start: 1 outliers final: 1 residues processed: 209 average time/residue: 0.2335 time to fit residues: 73.7184 Evaluate side-chains 161 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 127 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.091813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.070238 restraints weight = 60388.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.071955 restraints weight = 39802.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.073284 restraints weight = 29962.754| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14131 Z= 0.170 Angle : 0.626 12.513 19115 Z= 0.325 Chirality : 0.046 0.192 2106 Planarity : 0.005 0.067 2439 Dihedral : 6.639 77.204 1930 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.20), residues: 1694 helix: -1.01 (0.20), residues: 578 sheet: -1.24 (0.29), residues: 304 loop : -1.39 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 60 HIS 0.005 0.001 HIS B 30 PHE 0.022 0.002 PHE D 63 TYR 0.015 0.001 TYR D 146 ARG 0.006 0.001 ARG A 230 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 407) hydrogen bonds : angle 5.31246 ( 1155) covalent geometry : bond 0.00379 (14131) covalent geometry : angle 0.62650 (19115) *********************** 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 192 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.456 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: 0.8774 (mppt) cc_final: 0.8266 (mtmm) REVERT: A 118 ASN cc_start: 0.7881 (m110) cc_final: 0.7677 (t0) REVERT: A 147 LEU cc_start: 0.9183 (pp) cc_final: 0.8982 (pp) REVERT: A 243 ASN cc_start: 0.9055 (t0) cc_final: 0.8718 (p0) REVERT: A 276 PHE cc_start: 0.7646 (p90) cc_final: 0.7315 (p90) REVERT: A 408 CYS cc_start: 0.8544 (p) cc_final: 0.7847 (t) REVERT: C 354 MET cc_start: 0.7970 (pmm) cc_final: 0.7632 (pmm) REVERT: D 183 GLN cc_start: 0.9140 (tp40) cc_final: 0.8940 (tp-100) REVERT: E 61 LYS cc_start: 0.5444 (mttt) cc_final: 0.5198 (mttt) REVERT: E 86 ASN cc_start: 0.9081 (t0) cc_final: 0.8759 (p0) REVERT: E 125 GLU cc_start: 0.9401 (mt-10) cc_final: 0.8789 (mm-30) REVERT: E 166 ARG cc_start: 0.9142 (mmt-90) cc_final: 0.8295 (tpt170) REVERT: B 147 TYR cc_start: 0.8590 (t80) cc_final: 0.8215 (t80) REVERT: B 323 GLN cc_start: 0.9299 (tt0) cc_final: 0.9066 (tm-30) REVERT: B 353 MET cc_start: 0.7397 (mmp) cc_final: 0.6797 (mmm) REVERT: G 148 ARG cc_start: 0.5267 (mmm160) cc_final: 0.3246 (ptt180) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2415 time to fit residues: 70.6455 Evaluate side-chains 156 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 17 optimal weight: 8.9990 chunk 138 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 34 optimal weight: 0.0970 chunk 130 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** C 206 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.093770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.072123 restraints weight = 58214.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.074123 restraints weight = 38130.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.075619 restraints weight = 28449.942| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14131 Z= 0.106 Angle : 0.593 11.089 19115 Z= 0.304 Chirality : 0.045 0.184 2106 Planarity : 0.004 0.061 2439 Dihedral : 6.333 78.815 1930 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.20), residues: 1694 helix: -0.71 (0.21), residues: 570 sheet: -1.14 (0.29), residues: 316 loop : -1.26 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 60 HIS 0.005 0.001 HIS B 30 PHE 0.019 0.001 PHE F 101 TYR 0.017 0.001 TYR D 146 ARG 0.003 0.000 ARG A 230 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 407) hydrogen bonds : angle 5.01159 ( 1155) covalent geometry : bond 0.00234 (14131) covalent geometry : angle 0.59269 (19115) *********************** 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 197 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 1.672 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: A 18 LYS cc_start: 0.8778 (mppt) cc_final: 0.8282 (mtmm) REVERT: A 90 GLU cc_start: 0.9093 (tt0) cc_final: 0.8592 (tm-30) REVERT: A 118 ASN cc_start: 0.8045 (m110) cc_final: 0.7830 (t0) REVERT: A 147 LEU cc_start: 0.9088 (pp) cc_final: 0.8888 (pp) REVERT: A 270 ASP cc_start: 0.8031 (t0) cc_final: 0.7821 (t0) REVERT: A 408 CYS cc_start: 0.8506 (p) cc_final: 0.7693 (t) REVERT: C 235 MET cc_start: 0.7233 (mmp) cc_final: 0.6362 (mmp) REVERT: C 354 MET cc_start: 0.8056 (pmm) cc_final: 0.7761 (pmm) REVERT: E 86 ASN cc_start: 0.9041 (t0) cc_final: 0.8750 (p0) REVERT: E 125 GLU cc_start: 0.9390 (mt-10) cc_final: 0.8805 (mm-30) REVERT: E 166 ARG cc_start: 0.9044 (mmt-90) cc_final: 0.8205 (tpt170) REVERT: B 147 TYR cc_start: 0.8514 (t80) cc_final: 0.8105 (t80) REVERT: B 323 GLN cc_start: 0.9276 (tt0) cc_final: 0.8996 (tm-30) REVERT: B 353 MET cc_start: 0.7464 (mmp) cc_final: 0.6917 (mmm) REVERT: G 148 ARG cc_start: 0.5273 (mmm160) cc_final: 0.3369 (ptt180) outliers start: 1 outliers final: 1 residues processed: 197 average time/residue: 0.2294 time to fit residues: 69.0688 Evaluate side-chains 152 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 108 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** D 263 HIS ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.091984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.070468 restraints weight = 59501.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.072232 restraints weight = 39432.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.073473 restraints weight = 29503.920| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14131 Z= 0.153 Angle : 0.614 10.957 19115 Z= 0.316 Chirality : 0.046 0.192 2106 Planarity : 0.004 0.062 2439 Dihedral : 6.307 86.037 1930 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.07 % Allowed : 1.66 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.20), residues: 1694 helix: -0.60 (0.21), residues: 568 sheet: -1.24 (0.29), residues: 314 loop : -1.19 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 219 HIS 0.004 0.001 HIS D 254 PHE 0.018 0.002 PHE D 63 TYR 0.014 0.001 TYR D 146 ARG 0.004 0.000 ARG A 230 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 407) hydrogen bonds : angle 5.12513 ( 1155) covalent geometry : bond 0.00344 (14131) covalent geometry : angle 0.61357 (19115) *********************** 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 186 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 2.023 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: A 18 LYS cc_start: 0.8761 (mppt) cc_final: 0.8076 (mtmt) REVERT: A 90 GLU cc_start: 0.9147 (tt0) cc_final: 0.8561 (tm-30) REVERT: A 118 ASN cc_start: 0.8051 (m110) cc_final: 0.7841 (t0) REVERT: A 147 LEU cc_start: 0.9110 (pp) cc_final: 0.8895 (pp) REVERT: C 354 MET cc_start: 0.7957 (pmm) cc_final: 0.7724 (pmm) REVERT: E 61 LYS cc_start: 0.5751 (pttt) cc_final: 0.5524 (ptpt) REVERT: E 86 ASN cc_start: 0.9237 (t0) cc_final: 0.8778 (p0) REVERT: E 125 GLU cc_start: 0.9396 (mt-10) cc_final: 0.8816 (mm-30) REVERT: E 166 ARG cc_start: 0.9015 (mmt-90) cc_final: 0.8276 (tpt170) REVERT: B 147 TYR cc_start: 0.8484 (t80) cc_final: 0.8050 (t80) REVERT: B 353 MET cc_start: 0.7483 (mmp) cc_final: 0.6932 (mmm) REVERT: G 148 ARG cc_start: 0.5307 (mmm160) cc_final: 0.3387 (ptp90) REVERT: F 159 ILE cc_start: 0.9196 (mm) cc_final: 0.8807 (tp) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.2846 time to fit residues: 81.5898 Evaluate side-chains 151 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 148 optimal weight: 50.0000 chunk 134 optimal weight: 3.9990 chunk 75 optimal weight: 0.1980 chunk 105 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 11 optimal weight: 0.0670 chunk 142 optimal weight: 0.0000 chunk 7 optimal weight: 1.9990 overall best weight: 0.6526 ------------------------------------------------------------------------------- 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 108 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 = 0.3962 r_free = 0.3962 target = 0.094368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.071999 restraints weight = 58809.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.074151 restraints weight = 36712.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.075875 restraints weight = 26595.141| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14131 Z= 0.106 Angle : 0.600 10.931 19115 Z= 0.305 Chirality : 0.045 0.193 2106 Planarity : 0.004 0.061 2439 Dihedral : 6.130 87.971 1930 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.20), residues: 1694 helix: -0.52 (0.21), residues: 569 sheet: -1.11 (0.30), residues: 310 loop : -1.15 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 219 HIS 0.010 0.001 HIS B 30 PHE 0.023 0.001 PHE D 247 TYR 0.014 0.001 TYR D 146 ARG 0.007 0.000 ARG C 179 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 407) hydrogen bonds : angle 4.94515 ( 1155) covalent geometry : bond 0.00238 (14131) covalent geometry : angle 0.60042 (19115) *********************** 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 190 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.777 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: A 18 LYS cc_start: 0.8683 (mppt) cc_final: 0.8271 (mtmm) REVERT: A 34 CYS cc_start: 0.7566 (p) cc_final: 0.7305 (m) REVERT: A 90 GLU cc_start: 0.9365 (tt0) cc_final: 0.8833 (tm-30) REVERT: A 118 ASN cc_start: 0.8170 (m110) cc_final: 0.7907 (t0) REVERT: A 147 LEU cc_start: 0.9206 (pp) cc_final: 0.8990 (pp) REVERT: A 408 CYS cc_start: 0.8682 (p) cc_final: 0.7924 (t) REVERT: C 189 MET cc_start: 0.8054 (ptp) cc_final: 0.7386 (ptt) REVERT: C 235 MET cc_start: 0.7727 (mmp) cc_final: 0.6086 (mmp) REVERT: D 183 GLN cc_start: 0.9054 (tp-100) cc_final: 0.8844 (tp-100) REVERT: E 86 ASN cc_start: 0.9264 (t0) cc_final: 0.8822 (p0) REVERT: E 125 GLU cc_start: 0.9369 (mt-10) cc_final: 0.8839 (mm-30) REVERT: E 166 ARG cc_start: 0.8893 (mmt-90) cc_final: 0.8076 (tpt170) REVERT: B 147 TYR cc_start: 0.8378 (t80) cc_final: 0.7981 (t80) REVERT: B 353 MET cc_start: 0.7244 (mmp) cc_final: 0.6760 (mmm) REVERT: G 148 ARG cc_start: 0.5105 (mmm160) cc_final: 0.3366 (ptp90) REVERT: F 159 ILE cc_start: 0.9265 (mm) cc_final: 0.8875 (tp) outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.2425 time to fit residues: 72.0466 Evaluate side-chains 158 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 102 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 150 optimal weight: 0.0870 overall best weight: 1.9162 ------------------------------------------------------------------------------- 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 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** 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 = 0.3923 r_free = 0.3923 target = 0.092221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.070768 restraints weight = 59107.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.072513 restraints weight = 38891.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.073892 restraints weight = 29206.727| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14131 Z= 0.143 Angle : 0.620 10.800 19115 Z= 0.320 Chirality : 0.046 0.192 2106 Planarity : 0.004 0.061 2439 Dihedral : 6.154 85.561 1930 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.20), residues: 1694 helix: -0.42 (0.21), residues: 569 sheet: -1.12 (0.29), residues: 315 loop : -1.12 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 60 HIS 0.010 0.001 HIS B 30 PHE 0.019 0.002 PHE F 90 TYR 0.011 0.001 TYR D 146 ARG 0.006 0.000 ARG A 230 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 407) hydrogen bonds : angle 5.09727 ( 1155) covalent geometry : bond 0.00323 (14131) covalent geometry : angle 0.61964 (19115) *********************** 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 183 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.765 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: 0.8751 (mppt) cc_final: 0.8489 (mtmt) REVERT: A 90 GLU cc_start: 0.9112 (tt0) cc_final: 0.8473 (tm-30) REVERT: A 118 ASN cc_start: 0.8133 (m110) cc_final: 0.7923 (t0) REVERT: C 189 MET cc_start: 0.7882 (ptp) cc_final: 0.7265 (ptt) REVERT: C 235 MET cc_start: 0.7707 (mmp) cc_final: 0.5982 (mmp) REVERT: D 76 LEU cc_start: 0.8919 (pt) cc_final: 0.8719 (pt) REVERT: E 70 TYR cc_start: 0.7349 (t80) cc_final: 0.7051 (t80) REVERT: E 86 ASN cc_start: 0.9012 (t0) cc_final: 0.8725 (p0) REVERT: E 125 GLU cc_start: 0.9397 (mt-10) cc_final: 0.8820 (mm-30) REVERT: E 166 ARG cc_start: 0.8992 (mmt-90) cc_final: 0.8344 (tpt170) REVERT: E 167 GLN cc_start: 0.8345 (pm20) cc_final: 0.7935 (pm20) REVERT: B 147 TYR cc_start: 0.8423 (t80) cc_final: 0.8061 (t80) REVERT: B 218 GLU cc_start: 0.8231 (mt-10) cc_final: 0.8012 (mt-10) REVERT: B 353 MET cc_start: 0.7456 (mmp) cc_final: 0.6913 (mmm) REVERT: G 148 ARG cc_start: 0.5322 (mmm160) cc_final: 0.3431 (ptp90) REVERT: F 159 ILE cc_start: 0.9231 (mm) cc_final: 0.8849 (tp) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2578 time to fit residues: 73.2854 Evaluate side-chains 145 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 152 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 49 optimal weight: 0.2980 chunk 63 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 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** B 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.093972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.072000 restraints weight = 59925.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.074159 restraints weight = 37490.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.075839 restraints weight = 27126.386| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14131 Z= 0.118 Angle : 0.614 10.543 19115 Z= 0.314 Chirality : 0.045 0.194 2106 Planarity : 0.004 0.060 2439 Dihedral : 6.041 82.771 1930 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.07 % Allowed : 0.27 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.20), residues: 1694 helix: -0.34 (0.22), residues: 569 sheet: -1.19 (0.29), residues: 307 loop : -1.09 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 60 HIS 0.011 0.001 HIS B 30 PHE 0.020 0.001 PHE D 247 TYR 0.012 0.001 TYR D 146 ARG 0.007 0.000 ARG D 267 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 407) hydrogen bonds : angle 5.03956 ( 1155) covalent geometry : bond 0.00267 (14131) covalent geometry : angle 0.61384 (19115) ********************** 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 187 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 2.256 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: 0.8694 (mppt) cc_final: 0.8378 (mtmt) REVERT: A 90 GLU cc_start: 0.9284 (tt0) cc_final: 0.8643 (tm-30) REVERT: A 374 ARG cc_start: 0.8281 (ptp90) cc_final: 0.8011 (ptt90) REVERT: C 189 MET cc_start: 0.8029 (ptp) cc_final: 0.7292 (ptt) REVERT: D 266 MET cc_start: 0.8354 (mmp) cc_final: 0.7831 (mmp) REVERT: E 70 TYR cc_start: 0.7550 (t80) cc_final: 0.7251 (t80) REVERT: E 86 ASN cc_start: 0.9141 (t0) cc_final: 0.8752 (p0) REVERT: E 113 LEU cc_start: 0.8535 (tt) cc_final: 0.8322 (tt) REVERT: E 125 GLU cc_start: 0.9377 (mt-10) cc_final: 0.8856 (mm-30) REVERT: E 166 ARG cc_start: 0.8882 (mmt-90) cc_final: 0.8180 (tpt170) REVERT: E 167 GLN cc_start: 0.8415 (pm20) cc_final: 0.7891 (pm20) REVERT: B 147 TYR cc_start: 0.8396 (t80) cc_final: 0.8009 (t80) REVERT: B 353 MET cc_start: 0.7210 (mmp) cc_final: 0.6764 (mmm) REVERT: G 148 ARG cc_start: 0.5231 (mmm160) cc_final: 0.3480 (ptp90) REVERT: F 148 GLU cc_start: 0.8922 (mp0) cc_final: 0.8525 (mp0) REVERT: F 159 ILE cc_start: 0.9275 (mm) cc_final: 0.8879 (tp) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.2877 time to fit residues: 83.4024 Evaluate side-chains 147 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 4.9990 chunk 125 optimal weight: 0.1980 chunk 116 optimal weight: 0.5980 chunk 166 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN ** A 144 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** B 323 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.093853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.071977 restraints weight = 60068.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.074146 restraints weight = 37347.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.075851 restraints weight = 26946.180| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14131 Z= 0.117 Angle : 0.597 10.444 19115 Z= 0.307 Chirality : 0.045 0.193 2106 Planarity : 0.004 0.061 2439 Dihedral : 5.966 76.920 1930 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.07 % Allowed : 0.13 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1694 helix: -0.29 (0.22), residues: 569 sheet: -1.24 (0.29), residues: 298 loop : -1.01 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 60 HIS 0.010 0.001 HIS B 30 PHE 0.018 0.001 PHE D 247 TYR 0.014 0.001 TYR D 64 ARG 0.003 0.000 ARG A 230 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 407) hydrogen bonds : angle 5.01096 ( 1155) covalent geometry : bond 0.00265 (14131) covalent geometry : angle 0.59744 (19115) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5187.78 seconds wall clock time: 94 minutes 45.92 seconds (5685.92 seconds total)