Starting phenix.real_space_refine on Thu Aug 6 21:37:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ukh_64239/08_2026/9ukh_64239.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ukh_64239/08_2026/9ukh_64239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ukh_64239/08_2026/9ukh_64239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ukh_64239/08_2026/9ukh_64239.map" model { file = "/net/cci-nas-00/data/ceres_data/9ukh_64239/08_2026/9ukh_64239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ukh_64239/08_2026/9ukh_64239.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 70 5.16 5 C 10714 2.51 5 N 3002 2.21 5 O 3186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16984 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2349 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 12, 'TRANS': 283} Chain breaks: 1 Chain: "B" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2342 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "C" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2361 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain breaks: 1 Chain: "D" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2466 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain: "E" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2475 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 12, 'TRANS': 300} Chain: "F" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2456 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 12, 'TRANS': 296} Chain breaks: 1 Chain: "G" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2439 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.41, per 1000 atoms: 0.20 Number of scatterers: 16984 At special positions: 0 Unit cell: (122.848, 132.62, 129.828, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 70 16.00 P 9 15.00 Mg 3 11.99 O 3186 8.00 N 3002 7.00 C 10714 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: 1.17 Conformation dependent library (CDL) restraints added in 610.1 milliseconds 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4012 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 25 sheets defined 48.0% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 50 through 62 removed outlier: 3.764A pdb=" N PHE A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.823A pdb=" N ILE A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 127 through 133 removed outlier: 3.639A pdb=" N GLN A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 147 through 159 removed outlier: 4.376A pdb=" N PHE A 152 " --> pdb=" O PRO A 148 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N VAL A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 removed outlier: 3.873A pdb=" N ARG A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 removed outlier: 3.844A pdb=" N VAL A 226 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 3.994A pdb=" N GLU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 284 removed outlier: 3.601A pdb=" N VAL A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 295 through 298 Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 50 through 64 Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.849A pdb=" N ILE B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 143 through 146 Processing helix chain 'B' and resid 147 through 157 removed outlier: 4.241A pdb=" N PHE B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL B 153 " --> pdb=" O ASP B 149 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 233 removed outlier: 3.599A pdb=" N VAL B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 261 removed outlier: 3.796A pdb=" N GLU B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA B 258 " --> pdb=" O MET B 254 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 283 removed outlier: 3.831A pdb=" N ALA B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.533A pdb=" N PHE B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 312 removed outlier: 4.452A pdb=" N ALA B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 50 through 64 Processing helix chain 'C' and resid 76 through 88 removed outlier: 3.713A pdb=" N ILE C 81 " --> pdb=" O LYS C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.532A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 134 Processing helix chain 'C' and resid 147 through 158 removed outlier: 3.814A pdb=" N PHE C 152 " --> pdb=" O PRO C 148 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL C 153 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 157 " --> pdb=" O VAL C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.698A pdb=" N ARG C 210 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 removed outlier: 3.560A pdb=" N ASN C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 261 removed outlier: 3.547A pdb=" N PHE C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 281 Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 299 through 315 removed outlier: 4.362A pdb=" N ALA C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.738A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 134 Processing helix chain 'D' and resid 143 through 146 Processing helix chain 'D' and resid 154 through 159 removed outlier: 3.554A pdb=" N GLU D 159 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 removed outlier: 3.536A pdb=" N MET D 208 " --> pdb=" O ASN D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 238 through 262 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.623A pdb=" N VAL D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 126 through 133 Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.579A pdb=" N GLY E 146 " --> pdb=" O TYR E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 146' Processing helix chain 'E' and resid 147 through 152 Processing helix chain 'E' and resid 153 through 156 removed outlier: 4.058A pdb=" N ARG E 156 " --> pdb=" O VAL E 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 156' Processing helix chain 'E' and resid 204 through 210 removed outlier: 3.706A pdb=" N ARG E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 233 Processing helix chain 'E' and resid 238 through 261 removed outlier: 3.756A pdb=" N ARG E 242 " --> pdb=" O ASN E 238 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU E 243 " --> pdb=" O ALA E 239 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE E 244 " --> pdb=" O GLU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 284 Processing helix chain 'E' and resid 287 through 294 Processing helix chain 'E' and resid 295 through 298 Processing helix chain 'E' and resid 301 through 315 removed outlier: 4.441A pdb=" N THR E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 50 through 64 Processing helix chain 'F' and resid 76 through 89 Processing helix chain 'F' and resid 102 through 107 removed outlier: 3.641A pdb=" N LEU F 106 " --> pdb=" O SER F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 133 removed outlier: 3.831A pdb=" N GLN F 133 " --> pdb=" O PRO F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 146 removed outlier: 3.745A pdb=" N GLY F 146 " --> pdb=" O TYR F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 143 through 146' Processing helix chain 'F' and resid 147 through 159 removed outlier: 3.548A pdb=" N PHE F 152 " --> pdb=" O PRO F 148 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE F 154 " --> pdb=" O VAL F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 233 removed outlier: 3.690A pdb=" N ASN F 227 " --> pdb=" O ASP F 223 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE F 228 " --> pdb=" O ASN F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 237 removed outlier: 3.500A pdb=" N GLN F 237 " --> pdb=" O LYS F 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 234 through 237' Processing helix chain 'F' and resid 238 through 262 removed outlier: 3.547A pdb=" N ARG F 242 " --> pdb=" O ASN F 238 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 283 removed outlier: 3.965A pdb=" N ALA F 281 " --> pdb=" O ALA F 277 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE F 282 " --> pdb=" O GLU F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 295 through 298 Processing helix chain 'F' and resid 300 through 303 Processing helix chain 'F' and resid 304 through 314 Processing helix chain 'G' and resid 330 through 335 removed outlier: 3.517A pdb=" N CYS G 335 " --> pdb=" O ALA G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 352 removed outlier: 3.567A pdb=" N LEU G 340 " --> pdb=" O ASP G 336 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG G 342 " --> pdb=" O ALA G 338 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG G 344 " --> pdb=" O LEU G 340 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY G 345 " --> pdb=" O ASP G 341 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE G 346 " --> pdb=" O ARG G 342 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS G 349 " --> pdb=" O GLY G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 373 removed outlier: 3.788A pdb=" N GLY G 359 " --> pdb=" O GLN G 355 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG G 360 " --> pdb=" O GLY G 356 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU G 361 " --> pdb=" O VAL G 357 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA G 371 " --> pdb=" O ARG G 367 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN G 372 " --> pdb=" O ARG G 368 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 395 removed outlier: 3.928A pdb=" N ILE G 394 " --> pdb=" O ARG G 390 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 390 through 395' Processing helix chain 'G' and resid 429 through 449 removed outlier: 3.744A pdb=" N LEU G 442 " --> pdb=" O CYS G 438 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG G 444 " --> pdb=" O ASP G 440 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU G 446 " --> pdb=" O LEU G 442 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU G 447 " --> pdb=" O ALA G 443 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG G 448 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS G 449 " --> pdb=" O THR G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 466 through 475 removed outlier: 4.340A pdb=" N GLU G 470 " --> pdb=" O GLY G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 501 Processing helix chain 'G' and resid 502 through 508 removed outlier: 3.968A pdb=" N LEU G 506 " --> pdb=" O ALA G 502 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY G 507 " --> pdb=" O ARG G 503 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU G 508 " --> pdb=" O ARG G 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 502 through 508' Processing helix chain 'G' and resid 509 through 511 No H-bonds generated for 'chain 'G' and resid 509 through 511' Processing helix chain 'G' and resid 519 through 532 removed outlier: 3.944A pdb=" N ALA G 523 " --> pdb=" O ILE G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 556 Processing helix chain 'G' and resid 559 through 575 removed outlier: 4.231A pdb=" N LEU G 563 " --> pdb=" O PRO G 559 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU G 567 " --> pdb=" O LEU G 563 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG G 568 " --> pdb=" O GLU G 564 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU G 575 " --> pdb=" O ILE G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 591 through 595 removed outlier: 3.663A pdb=" N TYR G 594 " --> pdb=" O VAL G 591 " (cutoff:3.500A) Processing helix chain 'G' and resid 605 through 621 removed outlier: 4.364A pdb=" N GLY G 609 " --> pdb=" O GLU G 605 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR G 612 " --> pdb=" O ALA G 608 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER G 617 " --> pdb=" O GLU G 613 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU G 621 " --> pdb=" O SER G 617 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 3.594A pdb=" N VAL A 30 " --> pdb=" O VAL A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 94 removed outlier: 6.652A pdb=" N VAL A 93 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU A 138 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR A 184 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE A 140 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 67 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 115 removed outlier: 3.668A pdb=" N GLU A 122 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 113 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 17 Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 96 removed outlier: 7.065A pdb=" N VAL B 93 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP B 141 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 95 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 67 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 113 removed outlier: 3.793A pdb=" N LYS B 109 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 113 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 164 through 165 Processing sheet with id=AA8, first strand: chain 'C' and resid 14 through 17 removed outlier: 3.702A pdb=" N VAL C 30 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 92 through 96 removed outlier: 6.456A pdb=" N VAL C 93 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP C 141 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL C 95 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU C 138 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR C 184 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE C 140 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 67 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 69 " --> pdb=" O ALA C 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 108 through 115 Processing sheet with id=AB2, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.590A pdb=" N LEU C 166 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C 171 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 14 through 17 removed outlier: 3.649A pdb=" N VAL D 30 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 92 through 96 removed outlier: 6.619A pdb=" N VAL D 93 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP D 141 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL D 95 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 67 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 108 through 114 removed outlier: 3.629A pdb=" N LYS D 109 " --> pdb=" O LYS D 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 164 through 165 removed outlier: 3.595A pdb=" N LEU D 164 " --> pdb=" O ILE D 173 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 14 through 17 Processing sheet with id=AB8, first strand: chain 'E' and resid 92 through 96 removed outlier: 6.851A pdb=" N VAL E 93 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASP E 141 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL E 95 " --> pdb=" O ASP E 141 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL E 67 " --> pdb=" O LEU E 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 108 through 115 removed outlier: 3.576A pdb=" N LYS E 109 " --> pdb=" O LYS E 124 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 120 " --> pdb=" O VAL E 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 164 through 166 removed outlier: 3.584A pdb=" N LEU E 164 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG E 171 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 96 removed outlier: 6.939A pdb=" N VAL F 93 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP F 141 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL F 95 " --> pdb=" O ASP F 141 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 108 through 115 removed outlier: 3.533A pdb=" N VAL F 113 " --> pdb=" O VAL F 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL F 118 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 164 through 165 removed outlier: 3.676A pdb=" N LEU F 164 " --> pdb=" O ILE F 173 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE F 173 " --> pdb=" O LEU F 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'G' and resid 327 through 329 removed outlier: 3.768A pdb=" N VAL G 329 " --> pdb=" O HIS G 489 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL G 491 " --> pdb=" O VAL G 329 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP G 422 " --> pdb=" O ILE G 544 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ALA G 584 " --> pdb=" O VAL G 599 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE G 601 " --> pdb=" O ALA G 584 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLY G 586 " --> pdb=" O ILE G 601 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 376 through 381 removed outlier: 6.231A pdb=" N TRP G 377 " --> pdb=" O ARG G 408 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG G 408 " --> pdb=" O TRP G 377 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE G 379 " --> pdb=" O GLN G 406 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN G 406 " --> pdb=" O PHE G 379 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR G 404 " --> pdb=" O LEU G 381 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.64 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: 5752 1.34 - 1.46: 3147 1.46 - 1.58: 8292 1.58 - 1.69: 15 1.69 - 1.81: 125 Bond restraints: 17331 Sorted by residual: bond pdb=" O3A ANP E 401 " pdb=" PB ANP E 401 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.44e+01 bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.84e+01 ... (remaining 17326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 23474 3.64 - 7.28: 88 7.28 - 10.92: 13 10.92 - 14.55: 0 14.55 - 18.19: 3 Bond angle restraints: 23578 Sorted by residual: angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 108.76 18.19 3.00e+00 1.11e-01 3.68e+01 angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 109.29 17.66 3.00e+00 1.11e-01 3.46e+01 angle pdb=" PB ANP E 401 " pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 126.95 110.43 16.52 3.00e+00 1.11e-01 3.03e+01 angle pdb=" C PHE D 314 " pdb=" CA PHE D 314 " pdb=" CB PHE D 314 " ideal model delta sigma weight residual 109.46 100.86 8.60 1.84e+00 2.95e-01 2.18e+01 angle pdb=" N ASP B 263 " pdb=" CA ASP B 263 " pdb=" C ASP B 263 " ideal model delta sigma weight residual 112.72 107.37 5.35 1.28e+00 6.10e-01 1.75e+01 ... (remaining 23573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.60: 8795 18.60 - 37.20: 1182 37.20 - 55.79: 313 55.79 - 74.39: 69 74.39 - 92.99: 28 Dihedral angle restraints: 10387 sinusoidal: 4187 harmonic: 6200 Sorted by residual: dihedral pdb=" C PHE D 314 " pdb=" N PHE D 314 " pdb=" CA PHE D 314 " pdb=" CB PHE D 314 " ideal model delta harmonic sigma weight residual -122.60 -109.40 -13.20 0 2.50e+00 1.60e-01 2.79e+01 dihedral pdb=" CA TYR A 63 " pdb=" C TYR A 63 " pdb=" N ASN A 64 " pdb=" CA ASN A 64 " ideal model delta harmonic sigma weight residual -180.00 -161.20 -18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASP A 50 " pdb=" C ASP A 50 " pdb=" N ARG A 51 " pdb=" CA ARG A 51 " ideal model delta harmonic sigma weight residual -180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 10384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2201 0.055 - 0.110: 425 0.110 - 0.165: 33 0.165 - 0.220: 3 0.220 - 0.275: 4 Chirality restraints: 2666 Sorted by residual: chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3' ANP E 401 " pdb=" C2' ANP E 401 " pdb=" C4' ANP E 401 " pdb=" O3' ANP E 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 2663 not shown) Planarity restraints: 3067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 147 " 0.056 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO C 148 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO C 148 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 148 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 313 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C ALA D 313 " 0.056 2.00e-02 2.50e+03 pdb=" O ALA D 313 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE D 314 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 223 " 0.014 2.00e-02 2.50e+03 2.70e-02 7.28e+00 pdb=" C ASP D 223 " -0.047 2.00e-02 2.50e+03 pdb=" O ASP D 223 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN D 224 " 0.016 2.00e-02 2.50e+03 ... (remaining 3064 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 150 2.55 - 3.13: 12886 3.13 - 3.72: 26112 3.72 - 4.31: 35572 4.31 - 4.90: 59560 Nonbonded interactions: 134280 Sorted by model distance: nonbonded pdb=" O2G ANP F 401 " pdb="MG MG F 402 " model vdw 1.958 2.170 nonbonded pdb=" O2G ANP E 401 " pdb="MG MG E 402 " model vdw 2.071 2.170 nonbonded pdb=" O1B ANP D 401 " pdb="MG MG D 402 " model vdw 2.138 2.170 nonbonded pdb=" O1B ANP F 401 " pdb=" O2G ANP F 401 " model vdw 2.188 3.040 nonbonded pdb=" OG1 THR F 79 " pdb=" O1A ANP F 401 " model vdw 2.212 3.040 ... (remaining 134275 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 9 through 318) selection = chain 'B' selection = (chain 'C' and (resid 9 through 188 or resid 204 through 318)) selection = (chain 'D' and (resid 9 through 188 or resid 204 through 318)) selection = (chain 'E' and (resid 9 through 188 or resid 204 through 318)) selection = (chain 'F' and (resid 9 through 188 or resid 204 through 318)) } 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: 6.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.120 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.005 0.149 17331 Z= 0.223 Angle : 0.633 18.193 23578 Z= 0.306 Chirality : 0.043 0.275 2666 Planarity : 0.004 0.085 3067 Dihedral : 18.560 92.988 6375 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.27 % Favored : 94.68 % Rotamer: Outliers : 0.72 % Allowed : 28.20 % Favored : 71.08 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.18), residues: 2107 helix: -0.24 (0.18), residues: 843 sheet: -0.69 (0.31), residues: 305 loop : -1.25 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 87 TYR 0.014 0.001 TYR F 143 PHE 0.023 0.001 PHE B 283 TRP 0.025 0.001 TRP G 499 HIS 0.004 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.22 (17331) covalent geometry : angle 0.63277 / 0.31 (23578) hydrogen bonds : bond 0.24011 / 15.72 ( 677) hydrogen bonds : angle 7.98766 / 5.60 ( 1938) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 408 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 ASP cc_start: 0.7357 (p0) cc_final: 0.7131 (p0) outliers start: 13 outliers final: 9 residues processed: 414 average time/residue: 0.1334 time to fit residues: 79.4971 Evaluate side-chains 417 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 408 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 169 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain G residue 615 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN A 235 HIS A 296 ASN D 227 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.137660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113466 restraints weight = 25082.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.117698 restraints weight = 12715.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.120538 restraints weight = 7776.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122328 restraints weight = 5353.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123614 restraints weight = 4080.452| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17331 Z= 0.146 Angle : 0.527 7.006 23578 Z= 0.276 Chirality : 0.041 0.143 2666 Planarity : 0.005 0.061 3067 Dihedral : 8.651 89.700 2462 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.70 % Favored : 94.26 % Rotamer: Outliers : 4.19 % Allowed : 25.11 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.19), residues: 2107 helix: 0.20 (0.18), residues: 855 sheet: -0.59 (0.31), residues: 309 loop : -1.23 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 87 TYR 0.013 0.001 TYR F 143 PHE 0.009 0.001 PHE B 283 TRP 0.011 0.001 TRP G 499 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (17331) covalent geometry : angle 0.52702 / 0.28 (23578) hydrogen bonds : bond 0.05013 / 3.28 ( 677) hydrogen bonds : angle 5.72049 / 4.05 ( 1938) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 395 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 MET cc_start: 0.6227 (mmp) cc_final: 0.5993 (mmp) REVERT: B 257 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.6316 (tm-30) REVERT: B 261 ASN cc_start: 0.6717 (m-40) cc_final: 0.6052 (m-40) REVERT: C 171 ARG cc_start: 0.7755 (ptt-90) cc_final: 0.7439 (ptt-90) REVERT: D 122 GLU cc_start: 0.8026 (pm20) cc_final: 0.7812 (pm20) REVERT: E 152 PHE cc_start: 0.8045 (m-80) cc_final: 0.7833 (m-80) REVERT: F 46 ASP cc_start: 0.7284 (p0) cc_final: 0.7010 (p0) REVERT: G 488 ARG cc_start: 0.6970 (ttm110) cc_final: 0.6597 (ttm110) REVERT: G 539 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7621 (pttm) outliers start: 76 outliers final: 47 residues processed: 434 average time/residue: 0.1305 time to fit residues: 83.0635 Evaluate side-chains 449 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 400 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 427 MET Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 522 GLU Chi-restraints excluded: chain G residue 539 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 116 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 74 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.9816 > 50:) chunk 101 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 HIS A 296 ASN D 80 HIS D 227 ASN E 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.137938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.113642 restraints weight = 25428.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117888 restraints weight = 12835.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.120747 restraints weight = 7843.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.122656 restraints weight = 5414.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123970 restraints weight = 4077.333| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17331 Z= 0.150 Angle : 0.519 9.584 23578 Z= 0.268 Chirality : 0.042 0.155 2666 Planarity : 0.004 0.050 3067 Dihedral : 6.884 85.833 2446 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.51 % Favored : 94.45 % Rotamer: Outliers : 4.91 % Allowed : 24.67 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.18), residues: 2107 helix: 0.19 (0.18), residues: 865 sheet: -0.55 (0.30), residues: 319 loop : -1.30 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 19 TYR 0.013 0.001 TYR F 143 PHE 0.011 0.001 PHE C 123 TRP 0.013 0.001 TRP G 499 HIS 0.007 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (17331) covalent geometry : angle 0.51918 / 0.27 (23578) hydrogen bonds : bond 0.04256 / 2.77 ( 677) hydrogen bonds : angle 5.39617 / 3.82 ( 1938) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 393 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7727 (mtp180) REVERT: B 257 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6180 (tm-30) REVERT: B 261 ASN cc_start: 0.6769 (m-40) cc_final: 0.6155 (m-40) REVERT: D 122 GLU cc_start: 0.7961 (pm20) cc_final: 0.7561 (pm20) REVERT: F 46 ASP cc_start: 0.7293 (p0) cc_final: 0.6975 (p0) REVERT: G 364 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7220 (mtt90) REVERT: G 488 ARG cc_start: 0.6903 (ttm110) cc_final: 0.6542 (ttm110) REVERT: G 509 MET cc_start: 0.7497 (tmm) cc_final: 0.6308 (tmm) outliers start: 89 outliers final: 56 residues processed: 445 average time/residue: 0.1291 time to fit residues: 83.8454 Evaluate side-chains 451 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 393 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 522 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 73 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 16 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 146 optimal weight: 0.0870 chunk 89 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 ASN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS A 296 ASN B 227 ASN D 80 HIS D 227 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.135674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111462 restraints weight = 25400.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.115638 restraints weight = 12937.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118458 restraints weight = 7956.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120239 restraints weight = 5526.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.121442 restraints weight = 4228.367| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 17331 Z= 0.223 Angle : 0.552 7.316 23578 Z= 0.288 Chirality : 0.043 0.168 2666 Planarity : 0.005 0.053 3067 Dihedral : 6.624 87.340 2444 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.31 % Favored : 93.64 % Rotamer: Outliers : 5.85 % Allowed : 24.34 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.18), residues: 2107 helix: 0.07 (0.18), residues: 863 sheet: -0.62 (0.29), residues: 325 loop : -1.32 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 87 TYR 0.017 0.001 TYR F 47 PHE 0.013 0.001 PHE D 179 TRP 0.015 0.001 TRP G 499 HIS 0.005 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (17331) covalent geometry : angle 0.55165 / 0.29 (23578) hydrogen bonds : bond 0.04583 / 3.01 ( 677) hydrogen bonds : angle 5.39458 / 3.83 ( 1938) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 416 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7694 (mtp180) REVERT: E 198 HIS cc_start: 0.7986 (OUTLIER) cc_final: 0.7696 (t-90) REVERT: F 303 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7373 (mtp-110) REVERT: G 488 ARG cc_start: 0.6864 (ttm110) cc_final: 0.6518 (ttm110) REVERT: G 509 MET cc_start: 0.7501 (tmm) cc_final: 0.6426 (tmm) REVERT: G 539 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7525 (pttm) outliers start: 106 outliers final: 72 residues processed: 474 average time/residue: 0.1315 time to fit residues: 90.7338 Evaluate side-chains 489 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 413 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 427 MET Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 539 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 136 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 HIS A 296 ASN D 80 HIS D 227 ASN D 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.137643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.115352 restraints weight = 25023.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118843 restraints weight = 14263.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.121176 restraints weight = 9384.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.122628 restraints weight = 6818.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123776 restraints weight = 5394.194| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17331 Z= 0.144 Angle : 0.516 7.928 23578 Z= 0.269 Chirality : 0.042 0.151 2666 Planarity : 0.004 0.051 3067 Dihedral : 6.314 88.204 2444 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.27 % Favored : 94.68 % Rotamer: Outliers : 5.79 % Allowed : 24.94 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.18), residues: 2107 helix: 0.14 (0.18), residues: 868 sheet: -0.49 (0.30), residues: 310 loop : -1.27 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 87 TYR 0.015 0.001 TYR F 143 PHE 0.010 0.001 PHE G 458 TRP 0.016 0.001 TRP G 499 HIS 0.009 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (17331) covalent geometry : angle 0.51609 / 0.27 (23578) hydrogen bonds : bond 0.03860 / 2.53 ( 677) hydrogen bonds : angle 5.19329 / 3.68 ( 1938) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 406 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7806 (mtt-85) REVERT: B 103 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7767 (mtp180) REVERT: D 122 GLU cc_start: 0.7899 (pm20) cc_final: 0.7579 (pm20) REVERT: D 141 ASP cc_start: 0.7834 (m-30) cc_final: 0.7538 (m-30) REVERT: E 141 ASP cc_start: 0.7584 (m-30) cc_final: 0.7337 (m-30) REVERT: G 488 ARG cc_start: 0.6749 (ttm110) cc_final: 0.6499 (ttm110) REVERT: G 509 MET cc_start: 0.7432 (tmm) cc_final: 0.6389 (tmm) REVERT: G 539 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7496 (pttp) REVERT: G 543 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6747 (tmm) outliers start: 105 outliers final: 69 residues processed: 469 average time/residue: 0.1315 time to fit residues: 89.3070 Evaluate side-chains 477 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 405 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 543 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 HIS A 296 ASN E 80 HIS E 207 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.137333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115121 restraints weight = 25009.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118576 restraints weight = 14259.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.120930 restraints weight = 9389.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.122405 restraints weight = 6801.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.123522 restraints weight = 5381.810| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17331 Z= 0.163 Angle : 0.525 8.004 23578 Z= 0.273 Chirality : 0.042 0.170 2666 Planarity : 0.004 0.052 3067 Dihedral : 6.302 89.915 2444 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.93 % Rotamer: Outliers : 5.68 % Allowed : 25.00 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.18), residues: 2107 helix: 0.16 (0.18), residues: 869 sheet: -0.53 (0.30), residues: 310 loop : -1.24 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 87 TYR 0.014 0.001 TYR F 143 PHE 0.011 0.001 PHE A 179 TRP 0.019 0.001 TRP G 499 HIS 0.005 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (17331) covalent geometry : angle 0.52469 / 0.27 (23578) hydrogen bonds : bond 0.03899 / 2.55 ( 677) hydrogen bonds : angle 5.15841 / 3.65 ( 1938) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 414 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7937 (mtt-85) cc_final: 0.7580 (mtt-85) REVERT: A 256 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7816 (mtt180) REVERT: B 103 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7791 (mtp180) REVERT: D 94 ARG cc_start: 0.7453 (ttp80) cc_final: 0.7141 (ttp80) REVERT: D 142 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7237 (mt-10) REVERT: D 312 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7401 (mtm-85) REVERT: E 141 ASP cc_start: 0.7554 (m-30) cc_final: 0.7257 (m-30) REVERT: F 264 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7578 (mp) REVERT: F 303 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7715 (ttm110) REVERT: G 368 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7950 (ttm-80) REVERT: G 509 MET cc_start: 0.7401 (tmm) cc_final: 0.6377 (tmm) REVERT: G 543 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6737 (tmm) outliers start: 103 outliers final: 83 residues processed: 474 average time/residue: 0.1224 time to fit residues: 84.5199 Evaluate side-chains 499 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 413 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 427 MET Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 543 MET Chi-restraints excluded: chain G residue 600 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 71 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 187 optimal weight: 0.0470 chunk 199 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 200 optimal weight: 0.0670 chunk 156 optimal weight: 0.7980 chunk 162 optimal weight: 0.4980 chunk 198 optimal weight: 6.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 ASN C 204 ASN D 198 HIS E 80 HIS E 207 GLN ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 423 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.139332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.116684 restraints weight = 24899.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120355 restraints weight = 13744.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.122858 restraints weight = 8865.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124518 restraints weight = 6322.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125544 restraints weight = 4890.244| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17331 Z= 0.111 Angle : 0.509 8.063 23578 Z= 0.262 Chirality : 0.041 0.161 2666 Planarity : 0.004 0.050 3067 Dihedral : 6.127 89.650 2444 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.13 % Favored : 94.83 % Rotamer: Outliers : 5.46 % Allowed : 25.50 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 2107 helix: 0.23 (0.18), residues: 875 sheet: -0.46 (0.31), residues: 310 loop : -1.23 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 488 TYR 0.018 0.001 TYR A 236 PHE 0.010 0.001 PHE G 458 TRP 0.022 0.001 TRP G 499 HIS 0.009 0.001 HIS E 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (17331) covalent geometry : angle 0.50923 / 0.26 (23578) hydrogen bonds : bond 0.03438 / 2.25 ( 677) hydrogen bonds : angle 5.02365 / 3.55 ( 1938) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 405 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7778 (mtp180) REVERT: C 160 SER cc_start: 0.5686 (OUTLIER) cc_final: 0.5099 (t) REVERT: C 163 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7491 (mtp-110) REVERT: C 253 ASP cc_start: 0.7508 (m-30) cc_final: 0.7233 (m-30) REVERT: D 122 GLU cc_start: 0.7902 (pm20) cc_final: 0.7592 (pm20) REVERT: D 142 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7110 (mt-10) REVERT: E 197 TYR cc_start: 0.7316 (m-80) cc_final: 0.6895 (m-80) REVERT: E 208 MET cc_start: 0.7530 (tpp) cc_final: 0.7284 (mmm) REVERT: E 209 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7556 (t0) REVERT: F 264 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7556 (mp) REVERT: F 303 ARG cc_start: 0.7894 (ttm110) cc_final: 0.7651 (ttm110) REVERT: G 368 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.7955 (ttm-80) REVERT: G 488 ARG cc_start: 0.6815 (ttm110) cc_final: 0.6463 (ttm110) REVERT: G 499 TRP cc_start: 0.6500 (t60) cc_final: 0.6264 (t60) REVERT: G 503 ARG cc_start: 0.7847 (mtp-110) cc_final: 0.7636 (mtp85) REVERT: G 509 MET cc_start: 0.7408 (tmm) cc_final: 0.6376 (tmm) REVERT: G 526 TRP cc_start: 0.7805 (t60) cc_final: 0.7376 (t60) outliers start: 99 outliers final: 75 residues processed: 469 average time/residue: 0.1284 time to fit residues: 88.0011 Evaluate side-chains 477 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 398 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 211 TRP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 600 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 99 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 137 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 HIS A 296 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS E 207 GLN ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.115841 restraints weight = 24939.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119602 restraints weight = 13718.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.122048 restraints weight = 8805.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123742 restraints weight = 6313.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.124759 restraints weight = 4890.592| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17331 Z= 0.137 Angle : 0.526 8.115 23578 Z= 0.271 Chirality : 0.041 0.160 2666 Planarity : 0.004 0.051 3067 Dihedral : 6.115 88.890 2444 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.70 % Favored : 94.26 % Rotamer: Outliers : 5.30 % Allowed : 25.77 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.18), residues: 2107 helix: 0.21 (0.18), residues: 875 sheet: -0.36 (0.30), residues: 318 loop : -1.23 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 66 TYR 0.015 0.001 TYR F 143 PHE 0.010 0.001 PHE A 179 TRP 0.018 0.001 TRP G 499 HIS 0.005 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (17331) covalent geometry : angle 0.52555 / 0.27 (23578) hydrogen bonds : bond 0.03572 / 2.32 ( 677) hydrogen bonds : angle 5.03082 / 3.55 ( 1938) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 410 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ASP cc_start: 0.6900 (p0) cc_final: 0.6422 (p0) REVERT: B 103 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7800 (mtp180) REVERT: B 159 GLU cc_start: 0.7198 (mp0) cc_final: 0.6994 (mp0) REVERT: C 163 ARG cc_start: 0.7771 (mtm110) cc_final: 0.7552 (mtp-110) REVERT: D 94 ARG cc_start: 0.7493 (ttp80) cc_final: 0.7292 (ttp80) REVERT: D 122 GLU cc_start: 0.7909 (pm20) cc_final: 0.7593 (pm20) REVERT: E 197 TYR cc_start: 0.7340 (m-80) cc_final: 0.6905 (m-80) REVERT: E 208 MET cc_start: 0.7567 (tpp) cc_final: 0.7328 (mmm) REVERT: F 264 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7543 (mp) REVERT: F 303 ARG cc_start: 0.7950 (ttm110) cc_final: 0.7676 (ttm110) REVERT: G 368 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.7939 (ttm-80) REVERT: G 488 ARG cc_start: 0.6792 (ttm110) cc_final: 0.6405 (ttm110) REVERT: G 499 TRP cc_start: 0.6535 (t60) cc_final: 0.6306 (t60) REVERT: G 509 MET cc_start: 0.7479 (tmm) cc_final: 0.6436 (tmm) REVERT: G 526 TRP cc_start: 0.7819 (t60) cc_final: 0.7383 (t60) REVERT: G 543 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6724 (tmm) outliers start: 96 outliers final: 83 residues processed: 468 average time/residue: 0.1287 time to fit residues: 87.5692 Evaluate side-chains 490 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 404 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 211 TRP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain G residue 327 GLU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 427 MET Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 543 MET Chi-restraints excluded: chain G residue 600 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 62 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 147 optimal weight: 0.0570 chunk 121 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 296 ASN B 227 ASN C 64 ASN C 100 HIS ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.135623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111229 restraints weight = 25339.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.115443 restraints weight = 12725.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118276 restraints weight = 7766.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120076 restraints weight = 5377.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121383 restraints weight = 4089.538| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 17331 Z= 0.243 Angle : 0.591 9.441 23578 Z= 0.306 Chirality : 0.044 0.171 2666 Planarity : 0.005 0.052 3067 Dihedral : 6.397 86.381 2444 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.30 % Allowed : 25.99 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.18), residues: 2107 helix: 0.01 (0.17), residues: 878 sheet: -0.52 (0.29), residues: 338 loop : -1.30 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 171 TYR 0.017 0.001 TYR F 47 PHE 0.015 0.002 PHE F 152 TRP 0.018 0.002 TRP G 499 HIS 0.013 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 (17331) covalent geometry : angle 0.59104 / 0.31 (23578) hydrogen bonds : bond 0.04387 / 2.89 ( 677) hydrogen bonds : angle 5.22692 / 3.70 ( 1938) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 422 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ASP cc_start: 0.6911 (p0) cc_final: 0.6534 (p0) REVERT: B 103 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7719 (mtp180) REVERT: B 160 SER cc_start: 0.7104 (p) cc_final: 0.6866 (p) REVERT: C 253 ASP cc_start: 0.7611 (m-30) cc_final: 0.7329 (m-30) REVERT: D 94 ARG cc_start: 0.7459 (ttp80) cc_final: 0.7216 (ttp80) REVERT: D 122 GLU cc_start: 0.7942 (pm20) cc_final: 0.7574 (pm20) REVERT: D 243 GLU cc_start: 0.6645 (mm-30) cc_final: 0.6386 (mm-30) REVERT: F 51 ARG cc_start: 0.6735 (mtp85) cc_final: 0.6435 (mtp85) REVERT: F 94 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7281 (mtp85) REVERT: F 264 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7586 (mp) REVERT: F 303 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7677 (ttm110) REVERT: G 364 ARG cc_start: 0.7475 (mtt180) cc_final: 0.7254 (mtt90) REVERT: G 368 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.7931 (ttm-80) REVERT: G 488 ARG cc_start: 0.6861 (ttm110) cc_final: 0.6499 (ttm110) REVERT: G 499 TRP cc_start: 0.6707 (t60) cc_final: 0.6494 (t60) REVERT: G 509 MET cc_start: 0.7557 (tmm) cc_final: 0.6494 (tmm) REVERT: G 543 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6791 (tmm) outliers start: 96 outliers final: 82 residues processed: 479 average time/residue: 0.1253 time to fit residues: 87.5914 Evaluate side-chains 506 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 421 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 211 TRP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 427 MET Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 543 MET Chi-restraints excluded: chain G residue 600 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 206 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 196 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 HIS A 296 ASN B 227 ASN C 64 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.137670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115147 restraints weight = 24804.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118830 restraints weight = 13730.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.121272 restraints weight = 8838.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122827 restraints weight = 6312.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.123648 restraints weight = 4939.662| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17331 Z= 0.163 Angle : 0.563 8.491 23578 Z= 0.290 Chirality : 0.043 0.181 2666 Planarity : 0.005 0.051 3067 Dihedral : 6.274 84.247 2444 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.97 % Allowed : 26.49 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.18), residues: 2107 helix: 0.13 (0.18), residues: 873 sheet: -0.43 (0.29), residues: 333 loop : -1.29 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 87 TYR 0.014 0.001 TYR D 72 PHE 0.014 0.001 PHE C 123 TRP 0.017 0.001 TRP G 499 HIS 0.004 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (17331) covalent geometry : angle 0.56265 / 0.29 (23578) hydrogen bonds : bond 0.03834 / 2.51 ( 677) hydrogen bonds : angle 5.12510 / 3.62 ( 1938) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 414 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ASN cc_start: 0.7620 (t0) cc_final: 0.7238 (t0) REVERT: B 98 ASP cc_start: 0.6884 (p0) cc_final: 0.6505 (p0) REVERT: B 103 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7760 (mtp180) REVERT: C 253 ASP cc_start: 0.7569 (m-30) cc_final: 0.7296 (m-30) REVERT: D 94 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7164 (ttp80) REVERT: D 122 GLU cc_start: 0.7934 (pm20) cc_final: 0.7568 (pm20) REVERT: D 243 GLU cc_start: 0.6606 (mm-30) cc_final: 0.6342 (mm-30) REVERT: E 120 VAL cc_start: 0.8173 (p) cc_final: 0.7953 (t) REVERT: E 197 TYR cc_start: 0.7337 (m-80) cc_final: 0.6828 (m-80) REVERT: F 51 ARG cc_start: 0.6719 (mtp85) cc_final: 0.6417 (mtp85) REVERT: F 94 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7255 (mtp85) REVERT: F 303 ARG cc_start: 0.7984 (ttm110) cc_final: 0.7688 (ttm110) REVERT: G 488 ARG cc_start: 0.6794 (ttm110) cc_final: 0.6468 (ttm110) REVERT: G 509 MET cc_start: 0.7474 (tmm) cc_final: 0.6450 (tmm) REVERT: G 539 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7467 (pttp) REVERT: G 543 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6708 (tmm) outliers start: 90 outliers final: 80 residues processed: 469 average time/residue: 0.1302 time to fit residues: 88.5953 Evaluate side-chains 495 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 412 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 211 TRP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 427 MET Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 543 MET Chi-restraints excluded: chain G residue 600 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 111 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 132 optimal weight: 0.2980 chunk 73 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 168 optimal weight: 0.0270 chunk 19 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 99 optimal weight: 0.0980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 ASN C 64 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS ** G 372 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 = 0.3719 r_free = 0.3719 target = 0.138782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.115941 restraints weight = 24898.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119644 restraints weight = 13843.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122117 restraints weight = 8919.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123727 restraints weight = 6370.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124939 restraints weight = 4963.991| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17331 Z= 0.113 Angle : 0.544 8.783 23578 Z= 0.279 Chirality : 0.041 0.221 2666 Planarity : 0.004 0.050 3067 Dihedral : 6.071 83.287 2444 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.47 % Allowed : 27.10 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.19), residues: 2107 helix: 0.24 (0.18), residues: 878 sheet: -0.35 (0.30), residues: 324 loop : -1.29 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 87 TYR 0.024 0.001 TYR A 236 PHE 0.012 0.001 PHE C 123 TRP 0.039 0.001 TRP G 499 HIS 0.005 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (17331) covalent geometry : angle 0.54383 / 0.28 (23578) hydrogen bonds : bond 0.03387 / 2.21 ( 677) hydrogen bonds : angle 5.02236 / 3.55 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2799.00 seconds wall clock time: 48 minutes 49.54 seconds (2929.54 seconds total)